def histogram(download=None):
apps = current_user.user_apps
reset_info = check_session_app(session, "histogram", apps)
if reset_info:
flash(reset_info, 'error')
# INITIATE SESSION
session["filename"] = "Select file.."
plot_arguments = figure_defaults()
session["plot_arguments"] = plot_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "histogram"
"""
renders the plot on the fly.
https://gist.github.com/illume/1f19a2cf9f26425b1761b63d9506331f
"""
if request.method == 'POST':
try:
if request.files["inputsessionfile"]:
msg, plot_arguments, error = read_session_file(
request.files["inputsessionfile"], "histogram")
if error:
flash(msg, 'error')
return render_template('/apps/histogram.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
if request.files["inputargumentsfile"]:
msg, plot_arguments, error = read_argument_file(
request.files["inputargumentsfile"], "histogram")
if error:
flash(msg, 'error')
return render_template('/apps/histogram.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
# IF THE USER UPLOADS A NEW FILE
# THEN UPDATE THE SESSION FILE
# READ INPUT FILE
inputfile = request.files["inputfile"]
if inputfile:
filename = secure_filename(inputfile.filename)
if allowed_file(inputfile.filename):
df = read_tables(inputfile)
cols = df.columns.tolist()
# INDICATE THE USER TO SELECT THE COLUMNS TO PLOT AS HISTOGRAMS
session["plot_arguments"] = figure_defaults()
session["plot_arguments"]["cols"] = cols
sometext = "Please select the columns from which we will plot your histograms"
plot_arguments = session["plot_arguments"]
flash(sometext, 'info')
return render_template('/apps/histogram.html',
filename=filename,
apps=apps,
**plot_arguments)
else:
# IF UPLOADED FILE DOES NOT CONTAIN A VALID EXTENSION PLEASE UPDATE
error_msg = "You can can only upload files with the following extensions: 'xlsx', 'tsv', 'csv'. Please make sure the file '%s' \
has the correct format and respective extension and try uploadling it again." % filename
flash(error_msg, 'error')
return render_template('/apps/histogram.html',
filename="Select file..",
apps=apps,
**plot_arguments)
if "df" not in list(session.keys()):
error_msg = "No data to plot, please upload a data or session file."
flash(error_msg, 'error')
return render_template('/apps/histogram.html',
filename="Select file..",
apps=apps,
**plot_arguments)
if not request.files["inputsessionfile"] and not request.files[
"inputargumentsfile"]:
df = pd.read_json(session["df"])
cols = df.columns.tolist()
filename = session["filename"]
#IN CASE THE USER HAS UNSELECTED ALL THE COLUMNS THAT WE NEED TO PLOT THE HISTOGRAMS
if request.form.getlist("vals") == []:
filename = session["filename"]
session["plot_arguments"] = figure_defaults()
session["plot_arguments"]["cols"] = cols
sometext = "Please select the columns from which we will plot your histograms"
plot_arguments = session["plot_arguments"]
flash(sometext, 'info')
return render_template('/apps/histogram.html',
filename=filename,
apps=apps,
**plot_arguments)
#IF THE USER SELECTED THE COLUMNS TO BE PLOTTED FOR THE FIRST TIME,
#WE INITIALIZE THE DICTIONARY GROUPS SETTINGS
plot_arguments = session["plot_arguments"]
if plot_arguments["groups_settings"] == dict():
plot_arguments["vals"] = request.form.getlist("vals")
groups = plot_arguments["vals"]
groups.sort()
groups_settings = dict()
for group in groups:
groups_settings[group]={"name":group,\
"values":df[group],\
"label":group,\
"color_value":None,\
"color_rgb":"",\
"bins_value":"auto",\
"bins_number":"",\
"orientation_value":"vertical",\
"histtype_value":"bar",\
"linewidth":0.5,\
"linestyle_value":"solid",\
"line_color":None,\
"line_rgb":"",\
"fill_alpha":0.8,\
"density":".off",\
"cumulative":".off"}
plot_arguments["groups_settings"] = groups_settings
plot_arguments = read_request(request)
#CALL FIGURE FUNCTION
fig = make_figure(df, plot_arguments)
#TRANSFORM FIGURE TO BYTES AND BASE64 STRING
figfile = io.BytesIO()
plt.savefig(figfile, format='png')
plt.close()
figfile.seek(0) # rewind to beginning of file
figure_url = base64.b64encode(
figfile.getvalue()).decode('utf-8')
return render_template('/apps/histogram.html',
figure_url=figure_url,
filename=filename,
apps=apps,
**plot_arguments)
#IF THE USER HAS SELECTED NEW COLUMNS TO BE PLOTTED
# if plot_arguments["vals"]!=request.form.getlist("vals"):
#groups=plot_arguments["vals"]
groups = request.form.getlist("vals")
groups.sort()
groups_settings = dict()
for group in groups:
if group not in list(
plot_arguments["groups_settings"].keys()):
groups_settings[group]={"name":group,\
"label":group,\
"color_value":None,\
"color_rgb":"",\
"bins_value":"auto",\
"bins_number":"",\
"orientation_value":"vertical",\
"histtype_value":"bar",\
"linewidth":0.5,\
"linestyle_value":"solid",\
"line_color":None,\
"line_rgb":"",\
"fill_alpha":0.8,
"density":".off",\
"cumulative":".off"}
else:
groups_settings[group]={"name":group,\
"label":request.form["%s.label" %group],\
"color_value":request.form["%s.color_value" %group],\
"color_rgb":request.form["%s.color_rgb" %group],\
"bins_value":request.form["%s.bins_value" %group],\
"bins_number":request.form["%s.bins_number" %group],\
"orientation_value":request.form["%s.orientation_value" %group],\
"histtype_value":request.form["%s.histtype_value" %group],\
"linewidth":request.form["%s.linewidth" %group],\
"linestyle_value":request.form["%s.linestyle_value" %group],\
"line_color":request.form["%s.line_color" %group],\
"line_rgb":request.form["%s.line_rgb" %group],\
"fill_alpha":request.form["%s.fill_alpha" %group]}
#If the user does not tick the options the arguments do not appear as keys in request.form
if "%s.density" % group in request.form.keys():
groups_settings[group][
"density"] = "on" #request.form["%s.density" %group]
else:
groups_settings[group]["density"] = "off"
if "%s.cumulative" % group in request.form.keys():
groups_settings[group][
"cumulative"] = "on" #request.form["%s.cumulative" %group]
else:
groups_settings[group]["cumulative"] = "off"
plot_arguments["groups_settings"] = groups_settings
plot_arguments = read_request(request)
#session["plot_arguments"]=plot_arguments
# MAKE SURE WE HAVE THE LATEST ARGUMENTS FOR THIS SESSION
filename = session["filename"]
plot_arguments = session["plot_arguments"]
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
#CALL FIGURE FUNCTION
# try:
fig = make_figure(df, plot_arguments)
#TRANSFORM FIGURE TO BYTES AND BASE64 STRING
figfile = io.BytesIO()
plt.savefig(figfile, format='png')
plt.close()
figfile.seek(0) # rewind to beginning of file
figure_url = base64.b64encode(figfile.getvalue()).decode('utf-8')
return render_template('/apps/histogram.html',
figure_url=figure_url,
filename=filename,
apps=apps,
**plot_arguments)
except Exception as e:
tb_str = handle_exception(e,
user=current_user,
eapp="histogram",
session=session)
flash(tb_str, 'traceback')
return render_template('/apps/histogram.html',
filename=session["filename"],
apps=apps,
**session["plot_arguments"])
else:
if download == "download":
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
plot_arguments = session["plot_arguments"]
# CALL FIGURE FUNCTION
fig = make_figure(df, plot_arguments)
figfile = io.BytesIO()
mimetypes = {
"png": 'image/png',
"pdf": "application/pdf",
"svg": "image/svg+xml"
}
plt.savefig(figfile, format=plot_arguments["downloadf"])
plt.close()
figfile.seek(0) # rewind to beginning of file
eventlog = UserLogging(email=current_user.email,
action="download figure histogram")
db.session.add(eventlog)
db.session.commit()
return send_file(figfile,
mimetype=mimetypes[plot_arguments["downloadf"]],
as_attachment=True,
attachment_filename=plot_arguments["downloadn"] +
"." + plot_arguments["downloadf"])
return render_template('apps/histogram.html',
filename=session["filename"],
apps=apps,
**session["plot_arguments"])
def violinplot(download=None):
apps = current_user.user_apps
plot_arguments = None
reset_info = check_session_app(session, "violinplot", apps)
if reset_info:
flash(reset_info, 'error')
# INITIATE SESSION
session["filename"] = "Select file.."
plot_arguments = figure_defaults()
session["plot_arguments"] = plot_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "violinplot"
if request.method == 'POST':
try:
if request.files["inputsessionfile"]:
msg, plot_arguments, error = read_session_file(
request.files["inputsessionfile"], "violinplot")
if error:
flash(msg, 'error')
return render_template('/apps/violinplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
if request.files["inputargumentsfile"]:
msg, plot_arguments, error = read_argument_file(
request.files["inputargumentsfile"], "violinplot")
if error:
flash(msg, 'error')
return render_template('/apps/violinplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
# IF THE USER UPLOADS A NEW FILE
# THEN UPDATE THE SESSION FILE
# READ INPUT FILE
inputfile = request.files["inputfile"]
if inputfile:
filename = secure_filename(inputfile.filename)
if allowed_file(inputfile.filename):
df = read_tables(inputfile)
cols = df.columns.tolist()
vals = [None] + cols
# sometext="Please select at least one numeric column to create your violin plot."
session["plot_arguments"]["cols"] = cols
session["plot_arguments"]["vals"] = vals
plot_arguments = session["plot_arguments"]
# plot_arguments=read_request(request)
# flash(sometext,'info')
return render_template('/apps/violinplot.html',
filename=filename,
apps=apps,
**plot_arguments)
else:
# IF UPLOADED FILE DOES NOT CONTAIN A VALID EXTENSION PLEASE UPDATE
error_msg = "You can can only upload files with the following extensions: 'xlsx', 'tsv', 'csv'. Please make sure the file '%s' \
has the correct format and respective extension and try uploadling it again." % filename
flash(error_msg, 'error')
return render_template('/apps/violinplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
if "df" not in list(session.keys()):
error_msg = "No data to plot, please upload a data or session file."
flash(error_msg, 'error')
return render_template('/apps/violinplot.html',
filename="Select file..",
apps=apps,
**plot_arguments)
# USER INPUT/PLOT_ARGUMENTS GETS UPDATED TO THE LATEST INPUT
plot_arguments = read_request(request)
# vals=request.form.getlist("vals")
vals = plot_arguments["vals"]
df = pd.read_json(session["df"])
filename = session["filename"]
#IN CASE THE USER HAS NOT SELECTED X_VAL or Y_VAL
if plot_arguments["x_val"] == "None" or plot_arguments[
"y_val"] == "None":
sometext = "Please select a valid value to plot in your X and Y axes"
plot_arguments = session["plot_arguments"]
plot_arguments["vals"] = vals
flash(sometext, 'info')
return render_template('/apps/iviolinplot.html',
filename=filename,
apps=apps,
**plot_arguments)
#IN CASE THE USER HAS UNSELECTED ALL THE COLUMNS THAT WE NEED TO PLOT THE VIOLINPLOT
if vals == []:
sometext = "Please select at least one numeric column from which we will plot your violinplot"
plot_arguments = session["plot_arguments"]
plot_arguments["vals"] = vals
flash(sometext, 'info')
return render_template('/apps/violinplot.html',
filename=filename,
apps=apps,
**plot_arguments)
#VERIFY THERE IS AT LEAST ONE NUMERIC COLUMN SELECTED BY THE USER
vals_copy = vals.copy()
vals_copy.remove(None)
if not any(df[vals_copy].dtypes.apply(is_numeric_dtype)):
sometext = "Remember that at least one of the columns you select has to be numeric"
session["plot_arguments"]["vals"] = [None] + vals
plot_arguments = session["plot_arguments"]
plot_arguments["vals"] = vals
flash(sometext, 'info')
return render_template('/apps/violinplot.html',
filename=filename,
apps=apps,
**plot_arguments)
# #IF THE USER HAS CHANGED THE COLUMNS TO PLOT
# if vals+["None"] != plot_arguments["vals"]:
# plot_arguments=figure_defaults()
# cols=df.columns.tolist()
# plot_arguments["vals"]=vals+["None"]
# plot_arguments["cols"]=cols
# session["plot_arguments"]=plot_arguments
# sometext="Please tweak the arguments of your violin plot"
# flash(sometext,'info')
# return render_template('/apps/violinplot.html' , filename=filename, apps=apps,**plot_arguments)
session["plot_arguments"] = plot_arguments
# MAKE SURE WE HAVE THE LATEST ARGUMENTS FOR THIS SESSION
#filename=session["filename"]
#plot_arguments=session["plot_arguments"]
#plot_arguments["vals"]=vals
#session["plot_arguments"]["vals"]=vals+["None"]
fig = make_figure(df, plot_arguments)
#TRANSFORM FIGURE TO BYTES AND BASE64 STRING
figfile = io.BytesIO()
plt.savefig(figfile, format='png')
plt.close()
figfile.seek(0) # rewind to beginning of file
figure_url = base64.b64encode(figfile.getvalue()).decode('utf-8')
return render_template('/apps/violinplot.html',
figure_url=figure_url,
filename=filename,
apps=apps,
**plot_arguments)
except Exception as e:
tb_str = handle_exception(e,
user=current_user,
eapp="violinplot",
session=session)
flash(tb_str, 'traceback')
if not plot_arguments:
plot_arguments = session["plot_arguments"]
return render_template('/apps/violinplot.html',
filename=session["filename"],
apps=apps,
**session["plot_arguments"])
else:
if download == "download":
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
plot_arguments = session["plot_arguments"]
# CALL FIGURE FUNCTION
fig = make_figure(df, plot_arguments)
figfile = io.BytesIO()
mimetypes = {
"png": 'image/png',
"pdf": "application/pdf",
"svg": "image/svg+xml"
}
plt.savefig(figfile, format=plot_arguments["downloadf"])
plt.close()
figfile.seek(0) # rewind to beginning of file
eventlog = UserLogging(email=current_user.email,
action="download figure violinplot")
db.session.add(eventlog)
db.session.commit()
return send_file(figfile,
mimetype=mimetypes[plot_arguments["downloadf"]],
as_attachment=True,
attachment_filename=plot_arguments["downloadn"] +
"." + plot_arguments["downloadf"])
return render_template('apps/violinplot.html',
filename=session["filename"],
apps=apps,
**session["plot_arguments"])
def heatmap(download=None):
"""
renders the plot on the fly.
https://gist.github.com/illume/1f19a2cf9f26425b1761b63d9506331f
"""
apps=current_user.user_apps
plot_arguments=None
reset_info=check_session_app(session,"heatmap",apps)
if reset_info:
flash(reset_info,'error')
# INITIATE SESSION
session["filename"]="Select file.."
plot_arguments=figure_defaults()
session["plot_arguments"]=plot_arguments
session["COMMIT"]=app.config['COMMIT']
session["app"]="heatmap"
if request.method == 'POST':
try:
if request.files["inputsessionfile"] :
msg, plot_arguments, error=read_session_file(request.files["inputsessionfile"],"heatmap")
if error:
flash(msg,'error')
return render_template('/apps/heatmap.html' , filename=session["filename"],apps=apps, **plot_arguments)
flash(msg,"info")
if request.files["inputargumentsfile"] :
msg, plot_arguments, error=read_argument_file(request.files["inputargumentsfile"],"heatmap")
if error:
flash(msg,'error')
return render_template('/apps/heatmap.html' , filename=session["filename"], apps=apps, **plot_arguments)
flash(msg,"info")
if not request.files["inputsessionfile"] and not request.files["inputargumentsfile"] :
plot_arguments=read_request(request)
# IF THE UPLOADS A NEW FILE
# THAN UPDATE THE SESSION FILE
# READ INPUT FILE
inputfile = request.files["inputfile"]
if inputfile:
filename = secure_filename(inputfile.filename)
if allowed_file(inputfile.filename):
df=read_tables(inputfile)
cols=df.columns.tolist()
session["plot_arguments"]["xcols"]=cols
session["plot_arguments"]["ycols"]=cols
# IF THE USER HAS NOT YET CHOOSEN X AND Y VALUES THAN PLEASE SELECT
if (session["plot_arguments"]["yvals"] not in cols) | (session["plot_arguments"]["xvals"] not in cols):
if session["plot_arguments"]["xvals"] not in cols:
session["plot_arguments"]["xvals"]=cols[0]
session["plot_arguments"]["xvals_colors_list"]=["select a row.."]+df[session["plot_arguments"]["xvals"]].tolist()
if session["plot_arguments"]["yvals"] not in cols:
session["plot_arguments"]["yvals"]=cols[1:]
sometext="Please select which columns should be used for plotting."
plot_arguments=session["plot_arguments"]
flash(sometext,'info')
return render_template('/apps/heatmap.html' , filename=filename, apps=apps,**plot_arguments)
plot_arguments=session["plot_arguments"]
flash("New file uploaded.",'info')
return render_template('/apps/heatmap.html' , filename=filename, apps=apps,**plot_arguments)
else:
# IF UPLOADED FILE DOES NOT CONTAIN A VALID EXTENSION PLEASE UPDATE
error_message="You can can only upload files with the following extensions: 'xlsx', 'tsv', 'csv'. Please make sure the file '%s' \
has the correct format and respective extension and try uploadling it again." %filename
flash(error_message,'error')
return render_template('/apps/heatmap.html' , filename="Select file..", apps=apps, **plot_arguments)
if "df" not in list(session.keys()):
error_message="No data to plot, please upload a data or session file."
flash(error_message,'error')
return render_template('/apps/heatmap.html' , filename="Select file..", apps=apps, **plot_arguments)
# READ INPUT DATA FROM SESSION JSON
df=pd.read_json(session["df"])
if len(df) == 1:
session["plot_arguments"]["row_cluster"]="off"
flash("You only have one row. Row dendrogram is now off.")
if len(session["plot_arguments"]["yvals"]) == 1:
session["plot_arguments"]["col_cluster"]="off"
flash("You only have one column. Columns dendrogram is now off.")
session["plot_arguments"]["xvals_colors_list"]=["select a row.."]+df[request.form["xvals"]].tolist()
# MAKE SURE WE HAVE THE LATEST ARGUMENTS FOR THIS SESSION
filename=session["filename"]
plot_arguments=session["plot_arguments"]
# CALL FIGURE FUNCTION
fig, cols_cluster_numbers, index_cluster_numbers, df_=make_figure(df,plot_arguments)
# TRANSFORM FIGURE TO BYTES AND BASE64 STRING
figfile = io.BytesIO()
plt.savefig(figfile, format='png')
plt.close()
figfile.seek(0) # rewind to beginning of file
figure_url = base64.b64encode(figfile.getvalue()).decode('utf-8')
return render_template('/apps/heatmap.html', figure_url=figure_url, filename=filename, apps=apps, **plot_arguments)
except Exception as e:
tb_str=handle_exception(e,user=current_user,eapp="heatmap",session=session)
flash(tb_str,'traceback')
if not plot_arguments:
plot_arguments=session["plot_arguments"]
return render_template('/apps/heatmap.html', filename=filename, apps=apps, **plot_arguments)
else:
if download == "download":
# READ INPUT DATA FROM SESSION JSON
df=pd.read_json(session["df"])
plot_arguments=session["plot_arguments"]
# CALL FIGURE FUNCTION
fig, cols_cluster_numbers, index_cluster_numbers, df_=make_figure(df,plot_arguments)
figfile = io.BytesIO()
mimetypes={"png":'image/png',"pdf":"application/pdf","svg":"image/svg+xml"}
plt.savefig(figfile, format=plot_arguments["downloadf"])
plt.close()
figfile.seek(0) # rewind to beginning of file
eventlog = UserLogging(email=current_user.email,action="download figure heatmap")
db.session.add(eventlog)
db.session.commit()
return send_file(figfile, mimetype=mimetypes[plot_arguments["downloadf"]], as_attachment=True, attachment_filename=plot_arguments["downloadn"]+"."+plot_arguments["downloadf"] )
if download == "clusters":
plot_arguments=session["plot_arguments"]
if int(plot_arguments["n_cols_cluster"]) == 0:
fixed_cols=True
plot_arguments["n_cols_cluster"]=1
else:
fixed_cols=False
if int(plot_arguments["n_rows_cluster"]) == 0:
fixed_rows=True
plot_arguments["n_rows_cluster"]=1
else:
fixed_rows=False
# READ INPUT DATA FROM SESSION JSON
df=pd.read_json(session["df"])
plot_arguments=session["plot_arguments"]
# CALL FIGURE FUNCTION
fig, cols_cluster_numbers, index_cluster_numbers, df_=make_figure(df,plot_arguments)
excelfile = io.BytesIO()
EXC=pd.ExcelWriter(excelfile)
df_.to_excel(EXC,sheet_name="heatmap",index=None)
cols_cluster_numbers.to_excel(EXC,sheet_name="rows",index=None)
index_cluster_numbers.to_excel(EXC,sheet_name="cols",index=None)
EXC.save()
excelfile.seek(0)
if fixed_rows:
plot_arguments["n_rows_cluster"]=0
if fixed_cols:
plot_arguments["n_cols_cluster"]=0
eventlog = UserLogging(email=current_user.email,action="download figure heatmap clusters")
db.session.add(eventlog)
db.session.commit()
return send_file(excelfile, attachment_filename=plot_arguments["downloadn"]+".xlsx")
return render_template('apps/heatmap.html', filename=session["filename"], apps=apps, **session["plot_arguments"])
def lifespan(download=None):
apps = current_user.user_apps
plot_arguments = None
reset_info = check_session_app(session, "lifespan", apps)
if reset_info:
flash(reset_info, 'error')
# INITIATE SESSION
session["filename"] = "Select file.."
plot_arguments = figure_defaults()
session["plot_arguments"] = plot_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "lifespan"
if request.method == 'POST':
try:
if request.files["inputsessionfile"]:
msg, plot_arguments, error = read_session_file(
request.files["inputsessionfile"], "lifespan")
if error:
flash(msg, 'error')
return render_template('/apps/lifespan.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
if request.files["inputargumentsfile"]:
msg, plot_arguments, error = read_argument_file(
request.files["inputargumentsfile"], "lifespan")
if error:
flash(msg, 'error')
return render_template('/apps/lifespan.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
# IF THE UPLOADS A NEW FILE
# THAN UPDATE THE SESSION FILE
# READ INPUT FILE
inputfile = request.files["inputfile"]
if inputfile:
filename = secure_filename(inputfile.filename)
if allowed_file(inputfile.filename):
df = read_tables(inputfile)
cols = df.columns.tolist()
if session["plot_arguments"]["censors_col"] not in cols:
session["plot_arguments"]["censors_col"] = ["None"
] + cols
if session["plot_arguments"]["groups"] not in cols:
session["plot_arguments"]["groups"] = ["None"] + cols
# IF THE USER HAS NOT YET CHOOSEN X AND Y VALUES THAN PLEASE SELECT
if (session["plot_arguments"]["yvals"] not in cols):
session["plot_arguments"]["xcols"] = cols
session["plot_arguments"]["xvals"] = cols[0]
session["plot_arguments"]["ycols"] = cols
session["plot_arguments"]["yvals"] = cols[1:]
sometext = "Please select which columns should be used for plotting."
plot_arguments = session["plot_arguments"]
flash(sometext, 'info')
return render_template('/apps/lifespan.html',
filename=filename,
apps=apps,
**plot_arguments)
else:
# IF UPLOADED FILE DOES NOT CONTAIN A VALID EXTENSION PLEASE UPDATE
error_msg = "You can can only upload files with the following extensions: 'xlsx', 'tsv', 'csv'. Please make sure the file '%s' \
has the correct format and respective extension and try uploadling it again." % filename
flash(error_msg, 'error')
return render_template('/apps/lifespan.html',
filename="Select file..",
apps=apps,
**plot_arguments)
if not request.files["inputsessionfile"] and not request.files[
"inputargumentsfile"]:
# USER INPUT/PLOT_ARGUMENTS GETS UPDATED TO THE LATEST INPUT
# WITH THE EXCEPTION OF SELECTION LISTS
plot_arguments = session["plot_arguments"]
if plot_arguments["groups_value"] != request.form[
"groups_value"]:
if request.form["groups_value"] != "None":
df = pd.read_json(session["df"])
df[request.form["groups_value"]] = df[
request.form["groups_value"]].apply(
lambda x: secure_filename(str(x)))
df = df.astype(str)
session["df"] = df.to_json()
groups = df[request.form["groups_value"]]
groups = list(set(groups))
groups.sort()
plot_arguments["list_of_groups"] = groups
groups_settings = []
group_dic = {}
for group in groups:
group_dic={"name":group,\
"censor_marker_value":plot_arguments["censor_marker_value"], \
"censor_marker_size_val":plot_arguments["censor_marker_size_val"], \
"edgecolor":plot_arguments["edgecolor"], \
"edgecolor_write":"", \
"edge_linewidth":plot_arguments["edge_linewidth"], \
"markerc":plot_arguments["markerc"], \
"markerc_write":"", \
"marker_alpha":plot_arguments["marker_alpha"], \
"ci_alpha":plot_arguments["ci_alpha"], \
"linestyle_value":plot_arguments["linestyle_value"], \
"linestyle_write":"", \
"linewidth_write":plot_arguments["linewidth_write"], \
"line_color_value":plot_arguments["line_color_value"],\
"linecolor_write":"", \
"show_censors":plot_arguments["show_censors"], \
"Conf_Interval":plot_arguments["Conf_Interval"], \
"ci_legend":plot_arguments["ci_legend"], \
"ci_force_lines":plot_arguments["ci_force_lines"]}
groups_settings.append(group_dic)
plot_arguments["groups_settings"] = groups_settings
elif request.form["groups_value"] == "None":
plot_arguments["groups_settings"] = []
plot_arguments["list_of_groups"] = []
elif plot_arguments["groups_value"] != "None":
groups_settings = []
group_dic = {}
for group in plot_arguments["list_of_groups"]:
group_dic={"name":group,\
"censor_marker_value":request.form["%s.censor_marker_value" %group], \
"censor_marker_size_val":request.form["%s.censor_marker_size_val" %group], \
"edgecolor":request.form["%s.edgecolor" %group], \
"edgecolor_write":request.form["%s.edgecolor_write" %group], \
"edge_linewidth":request.form["%s.edge_linewidth" %group], \
"markerc":request.form["%s.markerc" %group], \
"markerc_write":request.form["%s.markerc_write" %group], \
"marker_alpha":request.form["%s.marker_alpha" %group], \
"ci_alpha":request.form["%s.ci_alpha" %group], \
"linestyle_value":request.form["%s.linestyle_value" %group], \
"linestyle_write":request.form["%s.linestyle_write" %group], \
"linewidth_write":request.form["%s.linewidth_write" %group], \
"line_color_value":request.form["%s.line_color_value" %group],\
"linecolor_write":request.form["%s.linecolor_write" %group]
}
if request.form.get("%s.show_censors" % group) == 'on':
group_dic["show_censors"] = 'on'
else:
group_dic["show_censors"] = 'off'
if request.form.get("%s.Conf_Interval" %
group) == 'on':
group_dic["Conf_Interval"] = 'on'
else:
group_dic["Conf_Interval"] = 'off'
if request.form.get("%s.ci_legend" % group) == 'on':
group_dic["ci_legend"] = 'on'
else:
group_dic["ci_legend"] = 'off'
if request.form.get("%s.ci_force_lines" %
group) == 'on':
group_dic["ci_force_lines"] = 'on'
else:
group_dic["ci_force_lines"] = 'off'
groups_settings.append(group_dic)
plot_arguments["groups_settings"] = groups_settings
session["plot_arguments"] = plot_arguments
plot_arguments = read_request(request)
if "df" not in list(session.keys()):
error_message = "No data to plot, please upload a data or session file."
flash(error_message, 'error')
return render_template('/apps/lifespan.html',
filename="Select file..",
apps=apps,
**plot_arguments)
# MAKE SURE WE HAVE THE LATEST ARGUMENTS FOR THIS SESSION
filename = session["filename"]
plot_arguments = session["plot_arguments"]
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
# CALL FIGURE FUNCTION
# try:
if str(plot_arguments["groups_value"]) == "None":
df_ls, fig = make_figure(df, plot_arguments)
df_ls = df_ls.astype(str)
session["df_ls"] = df_ls.to_json()
# TRANSFORM FIGURE TO BYTES AND BASE64 STRING
figfile = io.BytesIO()
plt.savefig(figfile, format='png')
plt.close()
figfile.seek(0) # rewind to beginning of file
figure_url = base64.b64encode(
figfile.getvalue()).decode('utf-8')
#return render_template('/apps/lifespan.html', figure_url=figure_url, filename=filename, apps=apps, **plot_arguments)
df_selected = df_ls[:50]
cols_to_format = df_selected.columns.tolist()
table_headers = cols_to_format
for c in cols_to_format:
df_selected[c] = df_selected[c].apply(lambda x: nFormat(x))
df_selected = list(df_selected.values)
df_selected = [list(s) for s in df_selected]
return render_template('/apps/lifespan.html',
figure_url=figure_url,
table_headers=table_headers,
table_contents=df_selected,
filename=filename,
apps=apps,
**plot_arguments)
elif str(plot_arguments["groups_value"]) != "None":
df_ls, fig, cph_stats, cph_coeffs = make_figure(
df, plot_arguments)
df_ls = df_ls.astype(str)
session["df_ls"] = df_ls.to_json()
cph_stats = cph_stats.astype(str)
session["cph_stats"] = cph_stats.to_json()
cph_coeffs = cph_coeffs.astype(str)
session["cph_coeffs"] = cph_coeffs.to_json()
# TRANSFORM FIGURE TO BYTES AND BASE64 STRING
figfile = io.BytesIO()
plt.savefig(figfile, format='png')
plt.close()
figfile.seek(0) # rewind to beginning of file
figure_url = base64.b64encode(
figfile.getvalue()).decode('utf-8')
df_selected = df_ls[:50]
cols_to_format = df_selected.columns.tolist()
table_headers = cols_to_format
for c in cols_to_format:
df_selected[c] = df_selected[c].apply(lambda x: nFormat(x))
df_selected = list(df_selected.values)
df_selected = [list(s) for s in df_selected]
df_coeffs = cph_coeffs[:50]
cols_to_format_coeffs = df_coeffs.columns.tolist()
table_headers_coeffs = cols_to_format_coeffs
for c in cols_to_format_coeffs:
df_coeffs[c] = df_coeffs[c].apply(lambda x: nFormat(x))
df_coeffs = list(df_coeffs.values)
df_coeffs = [list(s) for s in df_coeffs]
df_stats = cph_stats[:50]
cols_to_format_stats = df_stats.columns.tolist()
table_headers_stats = cols_to_format_stats
for c in cols_to_format_stats:
df_stats[c] = df_stats[c].apply(lambda x: nFormat(x))
df_stats = list(df_stats.values)
df_stats = [list(s) for s in df_stats]
return render_template(
'/apps/lifespan.html',
figure_url=figure_url,
table_headers=table_headers,
table_contents=df_selected,
table_headers_coeffs=table_headers_coeffs,
table_contents_coeff=df_coeffs,
table_headers_stats=table_headers_stats,
table_contents_stats=df_stats,
filename=filename,
apps=apps,
**plot_arguments)
except Exception as e:
tb_str = handle_exception(e,
user=current_user,
eapp="lifespan",
session=session)
filename = session["filename"]
flash(tb_str, 'traceback')
if not plot_arguments:
plot_arguments = session["plot_arguments"]
return render_template('/apps/lifespan.html',
filename=filename,
apps=apps,
**plot_arguments)
else:
if download == "download":
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
plot_arguments = session["plot_arguments"]
if str(plot_arguments["groups_value"]) == "None":
# CALL FIGURE FUNCTION
df_ls, fig = make_figure(df, plot_arguments)
elif str(plot_arguments["groups_value"]) != "None":
# CALL FIGURE FUNCTION
df_ls, fig, cph_coeff, cph_stats = make_figure(
df, plot_arguments)
figfile = io.BytesIO()
mimetypes = {
"png": 'image/png',
"pdf": "application/pdf",
"svg": "image/svg+xml"
}
plt.savefig(figfile, format=plot_arguments["download_fig"])
plt.close()
figfile.seek(0) # rewind to beginning of file
eventlog = UserLogging(email=current_user.email,
action="download figure lifespan curve")
db.session.add(eventlog)
db.session.commit()
return send_file(
figfile,
mimetype=mimetypes[plot_arguments["download_fig"]],
as_attachment=True,
attachment_filename=plot_arguments["downloadn_fig"] + "." +
plot_arguments["download_fig"])
if download == "results":
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
plot_arguments = session["plot_arguments"]
if str(plot_arguments["groups_value"]) == "None":
# CALL FIGURE FUNCTION
df_ls, fig = make_figure(df, plot_arguments)
elif str(plot_arguments["groups_value"]) != "None":
# CALL FIGURE FUNCTION
df_ls, fig, cph_coeff, cph_stats = make_figure(
df, plot_arguments)
eventlog = UserLogging(email=current_user.email,
action="download table survival analysis")
db.session.add(eventlog)
db.session.commit()
if plot_arguments["downloadf"] == "xlsx":
excelfile = io.BytesIO()
EXC = pd.ExcelWriter(excelfile)
df_ls.to_excel(EXC, sheet_name="survival_analysis", index=None)
EXC.save()
excelfile.seek(0)
return send_file(
excelfile,
attachment_filename=plot_arguments["downloadn"] + ".xlsx",
as_attachment=True)
elif plot_arguments["downloadf"] == "tsv":
return Response(df_ls.to_csv(sep="\t"),
mimetype="text/csv",
headers={
"Content-disposition":
"attachment; filename=%s.tsv" %
plot_arguments["downloadn"]
})
if download == "cph":
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
plot_arguments = session["plot_arguments"]
if str(plot_arguments["groups_value"]) != "None":
# CALL FIGURE FUNCTION
df_ls, fig, cph_coeff, cph_stats = make_figure(
df, plot_arguments)
eventlog = UserLogging(
email=current_user.email,
action="download table cox proportional hazard")
db.session.add(eventlog)
db.session.commit()
if plot_arguments["downloadf"] == "xlsx":
excelfile = io.BytesIO()
EXC = pd.ExcelWriter(excelfile)
cph_stats.to_excel(EXC, sheet_name="Statistics", index=None)
cph_coeff.to_excel(EXC,
sheet_name="CoxProportionalHazard_coeff",
index=None)
EXC.save()
excelfile.seek(0)
return send_file(
excelfile,
attachment_filename=plot_arguments["downloadn"] + ".xlsx",
as_attachment=True)
elif plot_arguments["downloadf"] == "tsv":
return Response(cph_coeff.to_csv(sep="\t", mode='a'),
mimetype="text/csv",
headers={
"Content-disposition":
"attachment; filename=%s.tsv" %
plot_arguments["downloadn"]
})
return render_template('apps/lifespan.html',
filename=session["filename"],
apps=apps,
**session["plot_arguments"])
def tsne(download=None):
apps = current_user.user_apps
plot_arguments = None
reset_info = check_session_app(session, "tsne", apps)
if reset_info:
flash(reset_info, 'error')
# INITIATE SESSION
session["filename"] = "Select file.."
plot_arguments = figure_defaults()
session["plot_arguments"] = plot_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "tsne"
if request.method == 'POST':
try:
if request.files["inputsessionfile"]:
msg, plot_arguments, error = read_session_file(
request.files["inputsessionfile"], "tsne")
if error:
flash(msg, 'error')
return render_template('/apps/tsne.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
if request.files["inputargumentsfile"]:
msg, plot_arguments, error = read_argument_file(
request.files["inputargumentsfile"], "tsne")
if error:
flash(msg, 'error')
return render_template('/apps/tsne.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
if not request.files["inputsessionfile"] and not request.files[
"inputargumentsfile"]:
plot_arguments = read_request(request)
if "df" in list(session.keys()):
available_rows = pd.read_json(session["df"])
if plot_arguments[
"xvals"] in available_rows.columns.tolist():
available_rows = available_rows[
plot_arguments["xvals"]].tolist()
available_rows = list(set(available_rows))
available_rows.sort()
plot_arguments["available_rows"] = available_rows
# UPDATE SESSION VALUES
session["plot_arguments"] = plot_arguments
# IF THE UPLOADS A NEW FILE
# THAN UPDATE THE SESSION FILE
# READ INPUT FILE
inputfile = request.files["inputfile"]
if inputfile:
filename = secure_filename(inputfile.filename)
if allowed_file(inputfile.filename):
df = read_tables(inputfile)
cols = df.columns.tolist()
# IF THE USER HAS NOT YET CHOOSEN X AND Y VALUES THAN PLEASE SELECT
if (session["plot_arguments"]["yvals"] not in cols):
session["plot_arguments"]["xcols"] = cols
session["plot_arguments"]["xvals"] = cols[0]
session["plot_arguments"]["ycols"] = cols
session["plot_arguments"]["yvals"] = cols[1:]
available_rows = pd.read_json(session["df"])
if plot_arguments[
"xvals"] in available_rows.columns.tolist():
available_rows = available_rows[
plot_arguments["xvals"]].tolist()
available_rows = list(set(available_rows))
available_rows.sort()
session["plot_arguments"][
"available_rows"] = available_rows
sometext = "Please select which columns should be used for plotting."
plot_arguments = session["plot_arguments"]
flash(sometext, 'info')
return render_template('/apps/tsne.html',
filename=filename,
apps=apps,
**plot_arguments)
else:
# IF UPLOADED FILE DOES NOT CONTAIN A VALID EXTENSION PLEASE UPDATE
error_msg = "You can can only upload files with the following extensions: 'xlsx', 'tsv', 'csv'. Please make sure the file '%s' \
has the correct format and respective extension and try uploadling it again." % filename
flash(error_msg, 'error')
return render_template('/apps/tsne.html',
filename="Select file..",
apps=apps,
**plot_arguments)
if "df" not in list(session.keys()):
error_message = "No data to plot, please upload a data or session file."
flash(error_message, 'error')
return render_template('/apps/tsne.html',
filename="Select file..",
apps=apps,
**plot_arguments)
# MAKE SURE WE HAVE THE LATEST ARGUMENTS FOR THIS SESSION
filename = session["filename"]
plot_arguments = session["plot_arguments"]
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
# CALL FIGURE FUNCTION
# try:
df_tsne = make_figure(df, plot_arguments)
df_tsne = df_tsne.astype(str)
session["df_tsne"] = df_tsne.to_json()
#features=features.astype(str)
#session["features"]=features.to_json()
df_selected = df_tsne[:50]
cols_to_format = df_selected.columns.tolist()
#cols_to_format=[ s for s in cols_to_format if s not in ["gene_id","gene_name"] ]
table_headers = [cols_to_format[0]]
for c in cols_to_format[1:]:
df_selected[c] = df_selected[c].apply(lambda x: nFormat(x))
#new_name=c.split(" - ")[0]+" - "+nFormat(float(c.split(" - ")[-1].split("%")[0]))+"%"
new_name = c
table_headers.append(new_name)
df_selected = list(df_selected.values)
df_selected = [list(s) for s in df_selected]
#features_selected=features[:50]
#cols_to_format=features_selected.columns.tolist()
#cols_to_format=[ s for s in cols_to_format if "key" not in s ]
#features_headers=features_selected.columns.tolist()
#for c in cols_to_format[1:]:
# features_selected[c]=features_selected[c].apply(lambda x: nFormat(x) )
#features_selected=features_selected.astype(str)
#features_selected=features_selected.replace("nan","")
#features_selected=list(features_selected.values)
#features_selected=[ list(s) for s in features_selected ]
return render_template('/apps/tsne.html',
table_headers=table_headers,
table_contents=df_selected,
filename=filename,
apps=apps,
**plot_arguments)
except Exception as e:
tb_str = handle_exception(e,
user=current_user,
eapp="tsne",
session=session)
filename = session["filename"]
flash(tb_str, 'traceback')
if not plot_arguments:
plot_arguments = session["plot_arguments"]
return render_template('/apps/tsne.html',
filename=filename,
apps=apps,
**plot_arguments)
else:
if download == "download":
plot_arguments = session["plot_arguments"]
# READ INPUT DATA FROM SESSION JSON
df_tsne = pd.read_json(session["df_tsne"])
#features=pd.read_json(session["features"])
# CALL FIGURE FUNCTION
eventlog = UserLogging(email=current_user.email,
action="download table tsne values")
db.session.add(eventlog)
db.session.commit()
if plot_arguments["downloadf"] == "xlsx":
excelfile = io.BytesIO()
EXC = pd.ExcelWriter(excelfile)
df_tsne.to_excel(EXC, sheet_name="tsne", index=None)
#features.to_excel(EXC,sheet_name="features", index=None)
EXC.save()
excelfile.seek(0)
return send_file(
excelfile,
attachment_filename=plot_arguments["downloadn"] + ".xlsx",
as_attachment=True)
elif plot_arguments["downloadf"] == "tsv":
return Response(df_tsne.to_csv(sep="\t"),
mimetype="text/csv",
headers={
"Content-disposition":
"attachment; filename=%s.tsv" %
plot_arguments["downloadn"]
})
if download == "scatter":
# READ INPUT DATA FROM SESSION JSON
df_tsne = pd.read_json(session["df_tsne"])
reset_info = check_session_app(session, "iscatterplot", apps)
if reset_info:
flash(reset_info, 'error')
# INITIATE SESSION
session["filename"] = "<from tSNE>"
plot_arguments = iscatterplot.figure_defaults()
session["COMMIT"] = app.config['COMMIT']
session["app"] = "iscatterplot"
df_tsne = df_tsne.astype(str)
session["df"] = df_tsne.to_json()
plot_arguments["xcols"] = df_tsne.columns.tolist()
plot_arguments["ycols"] = df_tsne.columns.tolist()
plot_arguments["groups"] = plot_arguments[
"groups"] + df_tsne.columns.tolist()
plot_arguments["labels_col"] = df_tsne.columns.tolist()
plot_arguments["xvals"] = df_tsne.columns.tolist()[1]
plot_arguments["yvals"] = df_tsne.columns.tolist()[2]
plot_arguments["labels_col_value"] = df_tsne.columns.tolist()[0]
plot_arguments["title"] = "tSNE"
plot_arguments["xlabel"] = df_tsne.columns.tolist()[1]
plot_arguments["ylabel"] = df_tsne.columns.tolist()[2]
session["plot_arguments"] = plot_arguments
return render_template('/apps/iscatterplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
return render_template('apps/tsne.html',
filename=session["filename"],
apps=apps,
**session["plot_arguments"])
def ihistogram(download=None):
apps = current_user.user_apps
plot_arguments = None
reset_info = check_session_app(session, "ihistogram", apps)
if reset_info:
flash(reset_info, 'error')
# INITIATE SESSION
session["filename"] = "Select file.."
plot_arguments = figure_defaults()
session["plot_arguments"] = plot_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "ihistogram"
"""
renders the plot on the fly.
https://gist.github.com/illume/1f19a2cf9f26425b1761b63d9506331f
"""
if request.method == 'POST':
try:
if request.files["inputsessionfile"]:
msg, plot_arguments, error = read_session_file(
request.files["inputsessionfile"], "ihistogram")
if error:
flash(msg, 'error')
return render_template('/apps/ihistogram.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
if request.files["inputargumentsfile"]:
msg, plot_arguments, error = read_argument_file(
request.files["inputargumentsfile"], "ihistogram")
if error:
flash(msg, 'error')
return render_template('/apps/ihistogram.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
# IF THE USER UPLOADS A NEW FILE
# THEN UPDATE THE SESSION FILE
# READ INPUT FILE
inputfile = request.files["inputfile"]
if inputfile:
filename = secure_filename(inputfile.filename)
if allowed_file(inputfile.filename):
df = read_tables(inputfile)
cols = df.columns.tolist()
# INDICATE THE USER TO SELECT THE COLUMNS TO PLOT AS HISTOGRAMS
session["plot_arguments"] = figure_defaults()
session["plot_arguments"]["cols"] = cols
sometext = "Please select the columns from which we will plot your iHistograms"
plot_arguments = session["plot_arguments"]
flash(sometext, 'info')
return render_template('/apps/ihistogram.html',
filename=filename,
apps=apps,
**plot_arguments)
else:
# IF UPLOADED FILE DOES NOT CONTAIN A VALID EXTENSION PLEASE UPDATE
error_msg = "You can can only upload files with the following extensions: 'xlsx', 'tsv', 'csv'. Please make sure the file '%s' \
has the correct format and respective extension and try uploadling it again." % filename
flash(error_msg, 'error')
return render_template('/apps/ihistogram.html',
filename="Select file..",
apps=apps,
**plot_arguments)
if not request.files["inputsessionfile"] and not request.files[
"inputargumentsfile"]:
df = pd.read_json(session["df"])
cols = df.columns.tolist()
filename = session["filename"]
#IN CASE THE USER HAS UNSELECTED ALL THE COLUMNS THAT WE NEED TO PLOT THE HISTOGRAMS
if request.form.getlist("vals") == []:
session["plot_arguments"] = figure_defaults()
session["plot_arguments"]["cols"] = cols
sometext = "Please select the columns from which we will plot your iHistograms"
plot_arguments = session["plot_arguments"]
flash(sometext, 'info')
return render_template('/apps/ihistogram.html',
filename=filename,
apps=apps,
**plot_arguments)
#IF THE USER SELECTED THE COLUMNS TO BE PLOTTED FOR THE FIRST TIME OR IF THE USER CHANGES FROM KDE TO HIST OR FROM HIST TO KDE
# if "kde" in request.form.keys():
# kde=True
# else:
# kde=False
# if "kde" in request.form.keys() and session["plot_arguments"]["kde"]=="on":
# kde=False
# elif "kde" not in request.form.keys() and session["plot_arguments"]["kde"] in [".off","off"]:
# kde=False
# else:
# kde=True
# if "kde" in request.form.keys():
# print("route!!!", session["plot_arguments"]["kde"])
# else:
# print("NO ROUTE", session["plot_arguments"]["kde"])
# set_histogram_groups
# set_kde_groups
# if (session["plot_arguments"]["vals"]!=request.form.getlist("vals")):
if ("kde" in request.form.keys()) and (
session["plot_arguments"]["groups_settings"]
== dict()):
# kde and have no groups settings
set_kde_groups = True
set_histogram_groups = False
session["plot_arguments"]["kde"] = "on"
elif ("kde" not in request.form.keys()) and (
session["plot_arguments"]["groups_settings"]
== dict()):
# histogram and no groups settings
set_kde_groups = False
set_histogram_groups = True
session["plot_arguments"]["kde"] = "off"
elif ("kde" in request.form.keys()) and (
session["plot_arguments"]["kde"] in [".off", "off"]):
# coming from histogram to kde
set_kde_groups = True
set_histogram_groups = False
session["plot_arguments"]["kde"] = "on"
elif ("kde" not in request.form.keys()) and (
session["plot_arguments"]["kde"] in [".on", "on"]):
# coming from kde to histogram
set_kde_groups = False
set_histogram_groups = True
session["plot_arguments"]["kde"] = "off"
else:
set_kde_groups = False
set_histogram_groups = False
session["plot_arguments"]["kde"] = "off"
# else:
# set_kde_groups=False
# set_histogram_groups=True
# print(set_kde_groups, set_histogram_groups)
# if (session["plot_arguments"]["vals"]!=request.form.getlist("vals")):# or (session["plot_arguments"]["groups_settings"] == dict()):
# # if session["plot_arguments"]["groups_settings"] == dict() or kde or session["plot_arguments"]["vals"]!=request.form.getlist("vals"):
if set_histogram_groups:
plot_arguments = session["plot_arguments"]
plot_arguments["vals"] = request.form.getlist("vals")
groups = plot_arguments["vals"]
groups.sort()
groups_settings = dict()
for group in groups:
groups_settings[group]={"name":group,\
"values":df[group],\
"label":group,\
"color_value":"None",\
"color_rgb":"",\
"histnorm":"",\
"orientation_value":"vertical",\
"linewidth":0.5,\
"linestyle_value":"solid",\
"line_color":"lightgrey",\
"line_rgb":"",\
"opacity":"0.8",\
"text":"",\
"bins_number":"",\
"hoverinfo":"all",\
"hover_bgcolor":"None",\
"hover_bordercolor":"None",\
"hover_align":"auto",\
"hover_fontfamily":"Default",\
"hover_fontsize":"12",\
"hover_fontcolor":"None",\
"histfunc":"count",\
"density":".off",\
"cumulative_direction":"increasing",\
"cumulative":".off"}
#plot_arguments=read_request(request)
plot_arguments["groups_settings"] = groups_settings
session["plot_arguments"] = plot_arguments
filename = session["filename"]
plot_arguments = session["plot_arguments"]
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
#CALL FIGURE FUNCTION
fig = make_figure(df, plot_arguments)
figure_url = json.dumps(fig,
cls=plotly.utils.PlotlyJSONEncoder)
return render_template('/apps/ihistogram.html',
figure_url=figure_url,
filename=filename,
apps=apps,
**plot_arguments)
elif set_kde_groups:
plot_arguments = session["plot_arguments"]
plot_arguments["vals"] = request.form.getlist("vals")
groups = plot_arguments["vals"]
groups.sort()
groups_settings = dict()
for group in groups:
groups_settings[group]={
"label":group,\
"color_value":"None",\
"color_rgb":"",\
}
plot_arguments = read_request(request)
plot_arguments["groups_settings"] = groups_settings
session["plot_arguments"] = plot_arguments
filename = session["filename"]
plot_arguments = session["plot_arguments"]
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
#CALL FIGURE FUNCTION
fig = make_figure(df, plot_arguments)
figure_url = json.dumps(fig,
cls=plotly.utils.PlotlyJSONEncoder)
return render_template('/apps/ihistogram.html',
figure_url=figure_url,
filename=filename,
apps=apps,
**plot_arguments)
if "df" not in list(session.keys()):
error_msg = "No data to plot, please upload a data or session file."
flash(error_msg, 'error')
if not plot_arguments:
plot_arguments = session["plot_arguments"]
return render_template('/apps/ihistogram.html',
filename="Select file..",
apps=apps,
**plot_arguments)
# MAKE SURE WE HAVE THE LATEST ARGUMENTS FOR THIS SESSION
plot_arguments = read_request(request)
# UPDATE VALUES FROM GROUPS_SETTINGS WHICH DO NOT GET UPDATED WITH THE READ_REQUEST FUNCTION
#plot_arguments=session["plot_arguments"]
groups = request.form.getlist("vals")
groups_settings = dict()
groups.sort()
#IF THE USER WANTS TO PLOT A REGULAR HISTOGRAM
if plot_arguments["kde"] != "on":
#FOR COLUMNS ALREADY SELECTED BY USER
for group in groups:
if group not in plot_arguments["groups_settings"].keys():
groups_settings[group]={"name":group,\
"label":request.form["%s.label" %group],\
"color_value":request.form["%s.color_value" %group],\
"color_rgb":request.form["%s.color_rgb" %group],\
"histnorm":request.form["%s.histnorm" %group],\
"orientation_value":request.form["%s.orientation_value" %group],\
"linewidth":request.form["%s.linewidth" %group],\
"linestyle_value":request.form["%s.linestyle_value" %group],\
"line_color":request.form["%s.line_color" %group],\
"line_rgb":request.form["%s.line_rgb" %group],\
"opacity":request.form["%s.opacity" %group],\
"text":request.form["%s.text" %group],\
"bins_number":request.form["%s.bins_number" %group],\
"hoverinfo":request.form["%s.hoverinfo" %group],\
"hover_bgcolor":request.form["%s.hover_bgcolor" %group],\
"hover_bordercolor":request.form["%s.hover_bordercolor" %group],\
"hover_align":request.form["%s.hover_align" %group],\
"hover_fontsize":request.form["%s.hover_fontsize" %group],\
"hover_fontcolor":request.form["%s.hover_fontcolor" %group],\
"hover_fontfamily":request.form["%s.hover_fontfamily" %group],\
"cumulative_direction":request.form["%s.cumulative_direction" %group],\
"histfunc":request.form["%s.histfunc" %group]
}
#If the user does not tick the options the arguments do not appear as keys in request.form
if "%s.density" % group in request.form.keys():
groups_settings[group]["density"] = request.form[
"%s.density" % group]
else:
groups_settings[group]["density"] = "off"
if "%s.cumulative" % group in request.form.keys():
groups_settings[group][
"cumulative"] = request.form["%s.cumulative" %
group]
else:
groups_settings[group]["cumulative"] = "off"
#NEW COLUMNS SELECTED BY USER
else:
groups_settings[group]={"name":group,\
"label":request.form["%s.label" %group],\
"color_value":request.form["%s.color_value" %group],\
"color_rgb":request.form["%s.color_rgb" %group],\
"histnorm":request.form["%s.histnorm" %group],\
"orientation_value":request.form["%s.orientation_value" %group],\
"linewidth":request.form["%s.linewidth" %group],\
"linestyle_value":request.form["%s.linestyle_value" %group],\
"line_color":request.form["%s.line_color" %group],\
"line_rgb":request.form["%s.line_rgb" %group],\
"opacity":request.form["%s.opacity" %group],\
"text":request.form["%s.text" %group],\
"bins_number":request.form["%s.bins_number" %group],\
"hoverinfo":request.form["%s.hoverinfo" %group],\
"hover_bgcolor":request.form["%s.hover_bgcolor" %group],\
"hover_bordercolor":request.form["%s.hover_bordercolor" %group],\
"hover_align":request.form["%s.hover_align" %group],\
"hover_fontsize":request.form["%s.hover_fontsize" %group],\
"hover_fontcolor":request.form["%s.hover_fontcolor" %group],\
"hover_fontfamily":request.form["%s.hover_fontfamily" %group],\
"cumulative_direction":request.form["%s.cumulative_direction" %group],\
"histfunc":request.form["%s.histfunc" %group]}
#If the user does not tick the options the arguments do not appear as keys in request.form
if "%s.density" % group in request.form.keys():
groups_settings[group]["density"] = request.form[
"%s.density" % group]
else:
groups_settings[group]["density"] = "off"
if "%s.cumulative" % group in request.form.keys():
groups_settings[group][
"cumulative"] = request.form["%s.cumulative" %
group]
else:
groups_settings[group]["cumulative"] = "off"
#IF THE USER WANTS TO PLOT A KDE PLOT
else:
plot_arguments = session["plot_arguments"]
plot_arguments["vals"] = request.form.getlist("vals")
groups = plot_arguments["vals"]
groups.sort()
groups_settings = dict()
for group in groups:
#FOR COLUMNS NEW COLUMNS SELECTED BY USER
if group not in plot_arguments["groups_settings"].keys():
for group in groups:
groups_settings[group]={"label":group,\
"color_value":"None",\
"color_rgb":""}
#FOR COLUMNS ALREADY SELECTED BY USER
else:
groups_settings[group]={"label":group,\
"color_value":request.form["%s.color_value" %group],\
"color_rgb":request.form["%s.color_rgb" %group]}
plot_arguments["groups_settings"] = groups_settings
session["plot_arguments"] = plot_arguments
filename = session["filename"]
plot_arguments = session["plot_arguments"]
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
#CALL FIGURE FUNCTION
fig = make_figure(df, plot_arguments)
figure_url = json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)
return render_template('/apps/ihistogram.html',
figure_url=figure_url,
filename=filename,
apps=apps,
**plot_arguments)
except Exception as e:
tb_str = handle_exception(e,
user=current_user,
eapp="ihistogram",
session=session)
flash(tb_str, 'traceback')
return render_template('/apps/ihistogram.html',
filename=session["filename"],
apps=apps,
**session["plot_arguments"])
else:
if download == "download":
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
plot_arguments = session["plot_arguments"]
# CALL FIGURE FUNCTION
fig = make_figure(df, plot_arguments)
pio.orca.config.executable = '/miniconda/bin/orca'
pio.orca.config.use_xvfb = True
figfile = io.BytesIO()
mimetypes = {
"png": 'image/png',
"pdf": "application/pdf",
"svg": "image/svg+xml"
}
pa_ = {}
for v in ["fig_height", "fig_width"]:
if plot_arguments[v] != "":
pa_[v] = False
elif plot_arguments[v]:
pa_[v] = float(plot_arguments[v])
else:
pa_[v] = False
if (pa_["fig_height"]) & (pa_["fig_width"]):
fig.write_image(figfile,
format=plot_arguments["downloadf"],
height=pa_["fig_height"],
width=pa_["fig_width"])
else:
fig.write_image(figfile, format=plot_arguments["downloadf"])
figfile.seek(0) # rewind to beginning of file
eventlog = UserLogging(email=current_user.email,
action="download figure ihistogram")
db.session.add(eventlog)
db.session.commit()
return send_file(figfile,
mimetype=mimetypes[plot_arguments["downloadf"]],
as_attachment=True,
attachment_filename=plot_arguments["downloadn"] +
"." + plot_arguments["downloadf"])
return render_template('apps/ihistogram.html',
filename=session["filename"],
apps=apps,
**session["plot_arguments"])
def iheatmap(download=None):
"""
renders the plot on the fly.
https://gist.github.com/illume/1f19a2cf9f26425b1761b63d9506331f
"""
apps = current_user.user_apps
plot_arguments = None
reset_info = check_session_app(session, "iheatmap", apps)
if reset_info:
flash(reset_info, 'error')
# INITIATE SESSION
session["filename"] = "Select file.."
plot_arguments = figure_defaults()
session["plot_arguments"] = plot_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "iheatmap"
if request.method == 'POST':
try:
if request.files["inputsessionfile"]:
msg, plot_arguments, error = read_session_file(
request.files["inputsessionfile"], "iheatmap")
if error:
flash(msg, 'error')
return render_template('/apps/iheatmap.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
if request.files["inputargumentsfile"]:
msg, plot_arguments, error = read_argument_file(
request.files["inputargumentsfile"], "iheatmap")
if error:
flash(msg, 'error')
return render_template('/apps/iheatmap.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
if not request.files["inputsessionfile"] and not request.files[
"inputargumentsfile"]:
plot_arguments = read_request(request)
if "df" in list(session.keys()):
available_rows = pd.read_json(session["df"])
if plot_arguments[
"xvals"] in available_rows.columns.tolist():
available_rows = available_rows[
plot_arguments["xvals"]].tolist()
available_rows = list(set(available_rows))
available_rows.sort()
plot_arguments["available_rows"] = available_rows
# UPDATE SESSION VALUES
session["plot_arguments"] = plot_arguments
# IF THE UPLOADS A NEW FILE
# THAN UPDATE THE SESSION FILE
# READ INPUT FILE
inputfile = request.files["inputfile"]
if inputfile:
filename = secure_filename(inputfile.filename)
if allowed_file(inputfile.filename):
df = read_tables(inputfile)
cols = df.columns.tolist()
# IF THE USER HAS NOT YET CHOOSEN X AND Y VALUES THAN PLEASE SELECT
if (session["plot_arguments"]["yvals"] not in cols):
session["plot_arguments"]["xcols"] = cols
session["plot_arguments"]["xvals"] = cols[0]
session["plot_arguments"]["ycols"] = cols
session["plot_arguments"]["yvals"] = cols[1:]
available_rows = pd.read_json(session["df"])
if plot_arguments[
"xvals"] in available_rows.columns.tolist():
available_rows = available_rows[
plot_arguments["xvals"]].tolist()
available_rows = list(set(available_rows))
available_rows.sort()
session["plot_arguments"][
"available_rows"] = available_rows
sometext = "Please select which columns should be used for plotting."
plot_arguments = session["plot_arguments"]
flash(sometext, 'info')
return render_template('/apps/iheatmap.html',
filename=filename,
apps=apps,
**plot_arguments)
else:
# IF UPLOADED FILE DOES NOT CONTAIN A VALID EXTENSION PLEASE UPDATE
error_msg = "You can can only upload files with the following extensions: 'xlsx', 'tsv', 'csv'. Please make sure the file '%s' \
has the correct format and respective extension and try uploadling it again." % filename
flash(error_msg, 'error')
return render_template('/apps/iheatmap.html',
filename="Select file..",
apps=apps,
**plot_arguments)
if "df" not in list(session.keys()):
error_msg = "No data to plot, please upload a data or session file."
flash(error_msg, 'error')
return render_template('/apps/iheatmap.html',
filename="Select file..",
apps=apps,
**plot_arguments)
# MAKE SURE WE HAVE THE LATEST ARGUMENTS FOR THIS SESSION
filename = session["filename"]
plot_arguments = session["plot_arguments"]
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
if len(df) == 1:
session["plot_arguments"]["row_cluster"] = "off"
flash("You only have one row. Row dendrogram is now off.")
if len(session["plot_arguments"]["yvals"]) == 1:
session["plot_arguments"]["col_cluster"] = "off"
flash(
"You only have one column. Columns dendrogram is now off.")
# CALL FIGURE FUNCTION
# try:
fig, cols_cluster_numbers, index_cluster_numbers, df_ = make_figure(
df, plot_arguments)
figure_url = json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)
return render_template('/apps/iheatmap.html',
figure_url=figure_url,
filename=filename,
apps=apps,
**plot_arguments)
except Exception as e:
tb_str = handle_exception(e,
user=current_user,
eapp="iheatmap",
session=session)
filename = session["filename"]
flash(tb_str, 'traceback')
if not plot_arguments:
plot_arguments = session["plot_arguments"]
return render_template('/apps/iheatmap.html',
filename=filename,
apps=apps,
**plot_arguments)
else:
if download == "download":
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
plot_arguments = session["plot_arguments"]
# CALL FIGURE FUNCTION
fig, cols_cluster_numbers, index_cluster_numbers, df_ = make_figure(
df, plot_arguments)
pio.orca.config.executable = '/miniconda/bin/orca'
pio.orca.config.use_xvfb = True
#pio.orca.config.save()
figfile = io.BytesIO()
mimetypes = {
"png": 'image/png',
"pdf": "application/pdf",
"svg": "image/svg+xml"
}
fig.write_image(figfile,
format=plot_arguments["downloadf"],
height=float(plot_arguments["fig_height"]),
width=float(plot_arguments["fig_width"]))
figfile.seek(0) # rewind to beginning of file
eventlog = UserLogging(email=current_user.email,
action="download figure iheatmap")
db.session.add(eventlog)
db.session.commit()
return send_file(figfile,
mimetype=mimetypes[plot_arguments["downloadf"]],
as_attachment=True,
attachment_filename=plot_arguments["downloadn"] +
"." + plot_arguments["downloadf"])
if download == "clusters":
plot_arguments = session["plot_arguments"]
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
# CALL FIGURE FUNCTION
fig, cols_cluster_numbers, index_cluster_numbers, df_ = make_figure(
df, plot_arguments)
excelfile = io.BytesIO()
EXC = pd.ExcelWriter(excelfile)
df_.to_excel(EXC, sheet_name="heatmap", index=None)
if type(cols_cluster_numbers) != type(None):
cols_cluster_numbers.to_excel(EXC,
sheet_name="rows",
index=None)
if type(index_cluster_numbers) != type(None):
index_cluster_numbers.to_excel(EXC,
sheet_name="cols",
index=None)
EXC.save()
excelfile.seek(0)
eventlog = UserLogging(email=current_user.email,
action="download figure heatmap clusters")
db.session.add(eventlog)
db.session.commit()
return send_file(excelfile,
attachment_filename=plot_arguments["downloadn"] +
".xlsx")
return render_template('apps/iheatmap.html',
filename=session["filename"],
apps=apps,
**session["plot_arguments"])
def venndiagram(download=None):
apps = current_user.user_apps
plot_arguments = None
reset_info = check_session_app(session, "venndiagram", apps)
if reset_info:
flash(reset_info, 'error')
plot_arguments = figure_defaults()
session["plot_arguments"] = plot_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "venndiagram"
if request.method == 'POST':
try:
if request.files["inputsessionfile"]:
msg, plot_arguments, error = read_session_file(
request.files["inputsessionfile"], "venndiagram")
if error:
flash(msg, 'error')
return render_template('/apps/venndiagram.html',
apps=apps,
**plot_arguments)
flash(msg, "info")
if request.files["inputargumentsfile"]:
msg, plot_arguments, error = read_argument_file(
request.files["inputargumentsfile"], "venndiagram")
if error:
flash(msg, 'error')
return render_template('/apps/venndiagram.html',
apps=apps,
**plot_arguments)
flash(msg, "info")
if not request.files["inputsessionfile"] and not request.files[
"inputargumentsfile"]:
plot_arguments = read_request(request)
i = 0
for set_index in ["set1", "set2", "set3"]:
if plot_arguments["%s_values" % set_index] != "":
i = i + 1
if i < 2:
error_msg = "No data to plot, please upload data."
flash(error_msg, 'error')
return render_template('/apps/venndiagram.html',
apps=apps,
**plot_arguments)
if ("." in str(session["plot_arguments"]["population_size"])) | (
"," in str(session["plot_arguments"]["population_size"])):
error_msg = "Population size needs to be an integer."
flash(error_msg, 'error')
return render_template('/apps/venndiagram.html',
apps=apps,
**plot_arguments)
# make sure we have the latest given arguments
plot_arguments = session["plot_arguments"]
# CALL FIGURE FUNCTION
fig, df, pvalues = make_figure(plot_arguments)
# TRANSFORM FIGURE TO BYTES AND BASE64 STRING
figfile = io.BytesIO()
plt.savefig(figfile, format='png')
plt.close()
figfile.seek(0) # rewind to beginning of file
figure_url = base64.b64encode(figfile.getvalue()).decode('utf-8')
if pvalues:
message = "Hypergeometric test:<br><br>"
for pvalue in list(pvalues.keys()):
samples_keys = list(pvalues[pvalue].keys())
message=message+str(pvalue)+":<br>"+\
"- %s: "%samples_keys[0] + str(pvalues[pvalue][samples_keys[0]])+"<br>"+\
"- %s: "%samples_keys[1] + str(pvalues[pvalue][samples_keys[1]])+"<br>"+\
"- n common: " + str(pvalues[pvalue]["common"])+"<br>"+\
"- n total: " + str(int(pvalues[pvalue]["total"]))+"<br>"+\
"- p value: " + str(pvalues[pvalue]["p value"])+"<br><br>"
flash(message)
return render_template('/apps/venndiagram.html',
figure_url=figure_url,
apps=apps,
**plot_arguments)
except Exception as e:
tb_str = handle_exception(e,
user=current_user,
eapp="venndiagram",
session=session)
flash(tb_str, 'traceback')
if not plot_arguments:
plot_arguments = session["plot_arguments"]
return render_template('/apps/venndiagram.html',
apps=apps,
**session["plot_arguments"])
else:
if download == "download":
plot_arguments = session["plot_arguments"]
# CALL FIGURE FUNCTION
fig, df, pvalues = make_figure(plot_arguments)
figfile = io.BytesIO()
mimetypes = {
"png": 'image/png',
"pdf": "application/pdf",
"svg": "image/svg+xml"
}
plt.savefig(figfile, format=plot_arguments["downloadf"])
plt.close()
figfile.seek(0) #rewind to beginning of file
eventlog = UserLogging(email=current_user.email,
action="download figure venndiagram")
db.session.add(eventlog)
db.session.commit()
return send_file(figfile,
mimetype=mimetypes[plot_arguments["downloadf"]],
as_attachment=True,
attachment_filename=plot_arguments["downloadn"] +
"." + plot_arguments["downloadf"])
if download == "data":
plot_arguments = session["plot_arguments"]
fig, df, pvalues = make_figure(plot_arguments)
if pvalues:
message = pd.DataFrame()
for pvalue in pvalues:
tmp = pd.DataFrame(pvalues[pvalue], index=[pvalue])
tmp.columns = [
"n group 1", "n group 2", "n common", "n total",
"p value"
]
message = pd.concat([message, tmp])
excelfile = io.BytesIO()
EXC = pd.ExcelWriter(excelfile)
df.to_excel(EXC, sheet_name="venndiagram", index=None)
if pvalues:
message.to_excel(EXC, sheet_name="hyperg.test", index=True)
EXC.save()
excelfile.seek(0)
eventlog = UserLogging(email=current_user.email,
action="download figure venndiagram data")
db.session.add(eventlog)
db.session.commit()
return send_file(excelfile,
attachment_filename=plot_arguments["downloadn"] +
".xlsx")
return render_template('/apps/venndiagram.html',
apps=apps,
**session["plot_arguments"])
def iviolinplot(download=None):
apps=current_user.user_apps
reset_info=check_session_app(session,"iviolinplot",apps)
if reset_info:
flash(reset_info,'error')
# INITIATE SESSION
session["filename"]="Select file.."
plot_arguments=figure_defaults()
session["plot_arguments"]=plot_arguments
session["COMMIT"]=app.config['COMMIT']
session["app"]="iviolinplot"
if request.method == 'POST' :
try:
if request.files["inputsessionfile"] :
msg, plot_arguments, error=read_session_file(request.files["inputsessionfile"],"iviolinplot")
if error:
flash(msg,'error')
return render_template('/apps/iviolinplot.html' , filename=session["filename"],apps=apps, **plot_arguments)
flash(msg,"info")
if request.files["inputargumentsfile"] :
msg, plot_arguments, error=read_argument_file(request.files["inputargumentsfile"],"iviolinplot")
if error:
flash(msg,'error')
return render_template('/apps/iviolinplot.html' , filename=session["filename"], apps=apps, **plot_arguments)
flash(msg,"info")
# IF THE USER UPLOADS A NEW FILE
# THEN UPDATE THE SESSION FILE
# READ INPUT FILE
inputfile = request.files["inputfile"]
if inputfile:
filename = secure_filename(inputfile.filename)
if allowed_file(inputfile.filename):
df=read_tables(inputfile)
cols=df.columns.tolist()
vals=[None]+cols
# sometext="Please select at least one numeric column to create your violin plot."
session["plot_arguments"]["cols"]=cols
session["plot_arguments"]["vals"]=vals
plot_arguments=session["plot_arguments"]
# plot_arguments=read_request(request)
# flash(sometext,'info')
return render_template('/apps/iviolinplot.html' , filename=filename, apps=apps,**plot_arguments)
else:
# IF UPLOADED FILE DOES NOT CONTAIN A VALID EXTENSION PLEASE UPDATE
error_msg="You can can only upload files with the following extensions: 'xlsx', 'tsv', 'csv'. Please make sure the file '%s' \
has the correct format and respective extension and try uploadling it again." %filename
flash(error_msg,'error')
return render_template('/apps/iviolinplot.html' , filename=session["filename"], apps=apps, **plot_arguments)
if "df" not in list(session.keys()):
error_msg="No data to plot, please upload a data or session file."
flash(error_msg,'error')
return render_template('/apps/iviolinplot.html' , filename="Select file..", apps=apps, **plot_arguments)
# if not request.files["inputsessionfile"] and not request.files["inputargumentsfile"] :
# USER INPUT/PLOT_ARGUMENTS GETS UPDATED TO THE LATEST INPUT
plot_arguments=read_request(request)
# vals=request.form.getlist("vals")
vals=plot_arguments["vals"]
df=pd.read_json(session["df"])
filename=session["filename"]
#IN CASE THE USER HAS NOT SELECTED X_VAL or Y_VAL
if plot_arguments["x_val"] == "None" or plot_arguments["y_val"]=="None":
sometext="Please select a valid value to plot in your X and Y axes"
plot_arguments=session["plot_arguments"]
plot_arguments["vals"]=vals
flash(sometext,'info')
return render_template('/apps/iviolinplot.html' , filename=filename, apps=apps,**plot_arguments)
session["plot_arguments"]=plot_arguments
#CALL FIGURE FUNCTION
fig=make_figure(df,plot_arguments)
figure_url = json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)
return render_template('/apps/iviolinplot.html', figure_url=figure_url, filename=filename, apps=apps, **plot_arguments)
except Exception as e:
tb_str=handle_exception(e,user=current_user,eapp="iviolinplot",session=session)
flash(tb_str,'traceback')
return render_template('/apps/iviolinplot.html', filename=session["filename"], apps=apps, **session["plot_arguments"])
else:
if download == "download":
# READ INPUT DATA FROM SESSION JSON
df=pd.read_json(session["df"])
plot_arguments=session["plot_arguments"]
# CALL FIGURE FUNCTION
fig=make_figure(df,plot_arguments)
figfile = io.BytesIO()
mimetypes={"png":'image/png',"pdf":"application/pdf","svg":"image/svg+xml"}
plt.savefig(figfile, format=plot_arguments["downloadf"])
plt.close()
figfile.seek(0) # rewind to beginning of file
eventlog = UserLogging(email=current_user.email,action="download figure iviolinplot")
db.session.add(eventlog)
db.session.commit()
return send_file(figfile, mimetype=mimetypes[plot_arguments["downloadf"]], as_attachment=True, attachment_filename=plot_arguments["downloadn"]+"."+plot_arguments["downloadf"] )
return render_template('apps/iviolinplot.html', filename=session["filename"], apps=apps, **session["plot_arguments"])
def aarnaseqlake(download=None):
apps = current_user.user_apps
if "aarnaseqlake" not in [s["link"] for s in apps]:
return redirect(url_for('index'))
reset_info = check_session_app(session, "aarnaseqlake", apps)
if reset_info:
flash(reset_info, 'error')
# INITIATE SESSION
session["filename"] = "Select file.."
session["plot_arguments"] = {}
session["plot_arguments"][
"path_to_files"] = "/flaski_private/aarnaseqlake/"
gedf = pd.read_csv(session["plot_arguments"]["path_to_files"] +
"gene_expression.tsv",
sep="\t",
index_col=[0])
results_files = pd.read_csv(
session["plot_arguments"]["path_to_files"] + "files2ids.tsv",
sep="\t")
genes = pd.read_csv(session["plot_arguments"]["path_to_files"] +
"genes.tsv",
sep="\t")
available_data_sets = list(set(results_files["Set"].tolist()))
available_data_sets.sort()
session["plot_arguments"]["available_data_sets"] = [
"all"
] + available_data_sets
session["plot_arguments"]["selected_data_sets"] = ["all"]
groups = list(set(results_files["Group"].tolist()))
groups.sort()
session["plot_arguments"]["available_groups"] = ["all"] + groups
session["plot_arguments"]["selected_groups"] = ["all"]
available_reps = list(set(results_files["Reps"].tolist()))
available_reps.sort()
session["plot_arguments"]["available_reps"] = ["all"] + available_reps
session["plot_arguments"]["selected_reps"] = ["all"]
available_gene_names = list(set(genes["gene_name"].tolist()))
available_gene_names.sort()
session["plot_arguments"][
"available_gene_names"] = available_gene_names
session["plot_arguments"]["selected_gene_names"] = ""
available_gene_ids = list(set(genes["gene_id"].tolist()))
available_gene_ids.sort()
session["plot_arguments"]["available_gene_ids"] = available_gene_ids
session["plot_arguments"]["selected_gene_ids"] = ""
session["plot_arguments"]["download_format"] = ["tsv", "xlsx"]
session["plot_arguments"]["download_format_value"] = "xlsx"
session["plot_arguments"]["download_name"] = "RNAseqLake"
session["plot_arguments"][
"session_download_name"] = "MySession.RNAseqLake"
session["plot_arguments"]["inputsessionfile"] = "Select file.."
session["plot_arguments"][
"session_argumentsn"] = "MyArguments.RNAseqLake"
session["plot_arguments"]["inputargumentsfile"] = "Select file.."
plot_arguments = session["plot_arguments"]
plot_arguments, df_metadata, df_dge, df_ge, siggenesdf = get_tables(
plot_arguments)
session["plot_arguments"] = plot_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "aarnaseqlake"
if request.method == 'POST':
try:
plot_arguments = read_request(request)
plot_arguments, df_metadata, df_dge, df_ge, siggenesdf = get_tables(
plot_arguments)
session["plot_arguments"] = plot_arguments
return render_template('/apps/aarnaseqlake.html',
apps=apps,
**plot_arguments)
except Exception as e:
tb_str = handle_exception(e,
user=current_user,
eapp="aarnaseqlake",
session=session)
flash(tb_str, 'traceback')
return render_template('/apps/aarnaseqlake.html',
apps=apps,
**plot_arguments)
else:
if download == "metadata":
plot_arguments = session["plot_arguments"]
plot_arguments, df_metadata, df_dge, df_ge, siggenesdf = get_tables(
plot_arguments)
eventlog = UserLogging(email=current_user.email,
action="download aarnaseqlake")
db.session.add(eventlog)
db.session.commit()
if plot_arguments["download_format_value"] == "xlsx":
outfile = io.BytesIO()
EXC = pd.ExcelWriter(outfile)
df_metadata.to_excel(EXC, sheet_name="metadata", index=None)
EXC.save()
outfile.seek(0)
return send_file(
outfile,
attachment_filename=plot_arguments["download_name"] +
".metadata." + plot_arguments["download_format_value"],
as_attachment=True)
elif plot_arguments["download_format_value"] == "tsv":
return Response(
df_metadata.to_csv(sep="\t"),
mimetype="text/csv",
headers={
"Content-disposition":
"attachment; filename=%s.tsv" %
(plot_arguments["download_name"] + ".metadata")
})
if download == "siggenes":
plot_arguments = session["plot_arguments"]
plot_arguments, df_metadata, df_dge, df_ge, siggenesdf = get_tables(
plot_arguments)
eventlog = UserLogging(email=current_user.email,
action="download aarnaseqlake")
db.session.add(eventlog)
db.session.commit()
if plot_arguments["download_format_value"] == "xlsx":
outfile = io.BytesIO()
EXC = pd.ExcelWriter(outfile)
siggenesdf.to_excel(EXC, sheet_name="sig.genes", index=None)
EXC.save()
outfile.seek(0)
return send_file(
outfile,
attachment_filename=plot_arguments["download_name"] +
".siggenesdf." + plot_arguments["download_format_value"],
as_attachment=True)
elif plot_arguments["download_format_value"] == "tsv":
return Response(
df_metadata.to_csv(sep="\t"),
mimetype="text/csv",
headers={
"Content-disposition":
"attachment; filename=%s.tsv" %
(plot_arguments["download_name"] + ".siggenesdf")
})
if download == "geneexpression":
plot_arguments = session["plot_arguments"]
plot_arguments, df_metadata, df_dge, df_ge, siggenesdf = get_tables(
plot_arguments)
GO = pd.read_csv(plot_arguments["path_to_files"] + "GO.tsv",
sep="\t")
GO.columns = ["gene_id", "go_id", "go_name", "go_definition"]
# for c in GO.columns.tolist():
# GO[c]=GO[c].apply(lambda x: fix_go(x) )
df_ge = pd.merge(df_ge, GO, on=["gene_id"], how="left")
eventlog = UserLogging(email=current_user.email,
action="download aarnaseqlake")
db.session.add(eventlog)
db.session.commit()
if plot_arguments["download_format_value"] == "xlsx":
outfile = io.BytesIO()
EXC = pd.ExcelWriter(outfile)
df_ge.to_excel(EXC, sheet_name="geneexp.", index=None)
EXC.save()
outfile.seek(0)
return send_file(
outfile,
attachment_filename=plot_arguments["download_name"] +
".gene_expression." +
plot_arguments["download_format_value"],
as_attachment=True)
elif plot_arguments["download_format_value"] == "tsv":
return Response(
df_ge.to_csv(sep="\t"),
mimetype="text/csv",
headers={
"Content-disposition":
"attachment; filename=%s.tsv" %
(plot_arguments["download_name"] + ".gene_expression")
})
if download == "dge":
plot_arguments = session["plot_arguments"]
plot_arguments, df_metadata, df_dge, df_ge, siggenesdf = get_tables(
plot_arguments)
GO = pd.read_csv(plot_arguments["path_to_files"] + "GO.tsv",
sep="\t")
GO.columns = ["gene_id", "go_id", "go_name", "go_definition"]
df_dge = pd.merge(df_dge, GO, on=["gene_id"], how="left")
for c in GO.columns.tolist():
GO[c] = GO[c].apply(lambda x: fix_go(x))
eventlog = UserLogging(email=current_user.email,
action="download aarnaseqlake")
db.session.add(eventlog)
db.session.commit()
if plot_arguments["download_format_value"] == "xlsx":
outfile = io.BytesIO()
EXC = pd.ExcelWriter(outfile)
df_dge.to_excel(EXC, sheet_name="dge", index=None)
EXC.save()
outfile.seek(0)
return send_file(
outfile,
attachment_filename=plot_arguments["download_name"] +
".dge." + plot_arguments["download_format_value"],
as_attachment=True)
elif plot_arguments["download_format_value"] == "tsv":
return Response(df_dge.to_csv(sep="\t"),
mimetype="text/csv",
headers={
"Content-disposition":
"attachment; filename=%s.tsv" %
(plot_arguments["download_name"] + ".dge")
})
if download == "MAplot":
plot_arguments = session["plot_arguments"]
plot_arguments, df_metadata, df_dge, df_ge, siggenesdf = get_tables(
plot_arguments)
if type(df_dge) != type(pd.DataFrame()):
flash(
"No differential available to perform gene expression for an MA plot.",
'error')
return render_template('apps/aarnaseqlake.html',
apps=apps,
**session["plot_arguments"])
reset_info = check_session_app(session, "iscatterplot", apps)
if reset_info:
flash(reset_info, 'error')
session["filename"] = "<from RNAseq lake>"
plot_arguments = iscatterplot.figure_defaults()
session["plot_arguments"] = plot_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "iscatterplot"
df_dge["log10(baseMean)"] = df_dge["baseMean"].apply(
lambda x: np.log10(x))
df_dge.loc[df_dge["padj"] <= 0.05, "Significant"] = "yes"
df_dge.loc[df_dge["padj"] > 0.05, "Significant"] = "no"
df_dge = df_dge.astype(str)
session["df"] = df_dge.to_json()
plot_arguments["xcols"] = df_dge.columns.tolist()
plot_arguments["ycols"] = df_dge.columns.tolist()
plot_arguments["groups"] = df_dge.columns.tolist()
plot_arguments["labels_col"] = df_dge.columns.tolist()
plot_arguments["xvals"] = "log10(baseMean)"
plot_arguments["yvals"] = "log2FoldChange"
plot_arguments["labels_col_value"] = "gene_name"
plot_arguments["groups_value"] = "Significant"
plot_arguments["list_of_groups"] = ["yes", "no"]
plot_arguments["title"] = "MA plot"
plot_arguments["xlabel"] = "log10(base Mean)"
plot_arguments["ylabel"] = "log2(FC)"
groups_settings = []
group_dic={"name":"yes",\
"markers":"4",\
"markersizes_col":"select a column..",\
"markerc":"red",\
"markerc_col":"select a column..",\
"markerc_write":plot_arguments["markerc_write"],\
"edge_linewidth":plot_arguments["edge_linewidth"],\
"edge_linewidth_col":"select a column..",\
"edgecolor":plot_arguments["edgecolor"],\
"edgecolor_col":"select a column..",\
"edgecolor_write":"",\
"marker":"circle",\
"markerstyles_col":"select a column..",\
"marker_alpha":"0.25",\
"markeralpha_col_value":"select a column.."}
groups_settings.append(group_dic)
group_dic={"name":"no",\
"markers":"4",\
"markersizes_col":"select a column..",\
"markerc":"black",\
"markerc_col":"select a column..",\
"markerc_write":plot_arguments["markerc_write"],\
"edge_linewidth":plot_arguments["edge_linewidth"],\
"edge_linewidth_col":"select a column..",\
"edgecolor":plot_arguments["edgecolor"],\
"edgecolor_col":"select a column..",\
"edgecolor_write":"",\
"marker":"circle",\
"markerstyles_col":"select a column..",\
"marker_alpha":"0.25",\
"markeralpha_col_value":"select a column.."}
groups_settings.append(group_dic)
plot_arguments["groups_settings"] = groups_settings
session["plot_arguments"] = plot_arguments
return render_template('/apps/iscatterplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
if download == "Volcanoplot":
plot_arguments = session["plot_arguments"]
plot_arguments, df_metadata, df_dge, df_ge, siggenesdf = get_tables(
plot_arguments)
if type(df_ge) != type(pd.DataFrame()):
flash(
"No differential available to perform gene expression for an MA plot.",
'error')
return render_template('apps/aarnaseqlake.html',
apps=apps,
**session["plot_arguments"])
reset_info = check_session_app(session, "iscatterplot", apps)
if reset_info:
flash(reset_info, 'error')
session["filename"] = "<from RNAseq lake>"
plot_arguments = iscatterplot.figure_defaults()
session["COMMIT"] = app.config['COMMIT']
session["app"] = "iscatterplot"
df_dge["-log10(padj)"] = df_dge["padj"].apply(
lambda x: np.log10(x) * -1)
df_dge.loc[df_dge["padj"] <= 0.05, "Significant"] = "yes"
df_dge.loc[df_dge["padj"] > 0.05, "Significant"] = "no"
df_dge = df_dge.astype(str)
session["df"] = df_dge.to_json()
plot_arguments["xcols"] = df_dge.columns.tolist()
plot_arguments["ycols"] = df_dge.columns.tolist()
plot_arguments["groups"] = df_dge.columns.tolist()
plot_arguments["labels_col"] = df_dge.columns.tolist()
plot_arguments["xvals"] = "log2FoldChange"
plot_arguments["yvals"] = "-log10(padj)"
plot_arguments["labels_col_value"] = "gene_name"
plot_arguments["groups_value"] = "Significant"
plot_arguments["list_of_groups"] = ["yes", "no"]
plot_arguments["title"] = "Volcano plot"
plot_arguments["xlabel"] = "log2(FC)"
plot_arguments["ylabel"] = "-log10(padj)"
groups_settings = []
group_dic={"name":"yes",\
"markers":"4",\
"markersizes_col":"select a column..",\
"markerc":"red",\
"markerc_col":"select a column..",\
"markerc_write":plot_arguments["markerc_write"],\
"edge_linewidth":plot_arguments["edge_linewidth"],\
"edge_linewidth_col":"select a column..",\
"edgecolor":plot_arguments["edgecolor"],\
"edgecolor_col":"select a column..",\
"edgecolor_write":"",\
"marker":"circle",\
"markerstyles_col":"select a column..",\
"marker_alpha":"0.25",\
"markeralpha_col_value":"select a column.."}
groups_settings.append(group_dic)
group_dic={"name":"no",\
"markers":"4",\
"markersizes_col":"select a column..",\
"markerc":"black",\
"markerc_col":"select a column..",\
"markerc_write":plot_arguments["markerc_write"],\
"edge_linewidth":plot_arguments["edge_linewidth"],\
"edge_linewidth_col":"select a column..",\
"edgecolor":plot_arguments["edgecolor"],\
"edgecolor_col":"select a column..",\
"edgecolor_write":"",\
"marker":"circle",\
"markerstyles_col":"select a column..",\
"marker_alpha":"0.25",\
"markeralpha_col_value":"select a column.."}
groups_settings.append(group_dic)
plot_arguments["groups_settings"] = groups_settings
session["plot_arguments"] = plot_arguments
return render_template('/apps/iscatterplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
if download == "iheatmap":
plot_arguments = session["plot_arguments"]
plot_arguments, df_metadata, df_dge, df_ge, siggenesdf = get_tables(
plot_arguments)
sig_genes = df_dge[df_dge["padj"] < 0.05]["gene_name"].tolist()
df_ge = df_ge[df_ge["gene_name"].isin(sig_genes)]
if type(df_ge) != type(pd.DataFrame()):
flash(
"No differential available to perform gene expression for an MA plot.",
'error')
return render_template('apps/aarnaseqlake.html',
apps=apps,
**session["plot_arguments"])
reset_info = check_session_app(session, "iheatmap", apps)
if reset_info:
flash(reset_info, 'error')
plot_arguments = iheatmap.figure_defaults()
session["filename"] = "<from RNAseq lake>"
session["plot_arguments"] = plot_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "iheatmap"
cols = df_ge.columns.tolist()
df_de = df_ge.astype(str)
session["df"] = df_ge.to_json()
plot_arguments["xcols"] = cols
plot_arguments["ycols"] = cols
plot_arguments["xvals"] = "gene_name"
available_rows = list(set(df_ge["gene_name"].tolist()))
available_rows.sort()
plot_arguments["available_rows"] = available_rows
plot_arguments["yvals"] = [
s for s in cols if s not in ["gene_name", "gene_id"]
]
plot_arguments["title"] = "Heatmap"
plot_arguments["zscore_value"] = "row"
plot_arguments["colorscale_value"] = 'bluered'
plot_arguments["lower_value"] = "-2"
plot_arguments["center_value"] = "0"
plot_arguments["upper_value"] = "2"
plot_arguments["lower_color"] = "blue"
plot_arguments["center_color"] = "white"
plot_arguments["upper_color"] = "red"
plot_arguments["col_cluster"] = "off"
plot_arguments["title_size_value"] = "25"
plot_arguments["color_bar_label"] = "z-score"
plot_arguments["findrowup"] = "10"
plot_arguments["findrowdown"] = "10"
plot_arguments["xticklabels"] = "on"
session["plot_arguments"] = plot_arguments
return render_template('/apps/iheatmap.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
return render_template('apps/aarnaseqlake.html',
apps=apps,
**session["plot_arguments"])
def david(download=None):
apps = current_user.user_apps
reset_info = check_session_app(session, "david", apps)
if reset_info:
flash(reset_info, 'error')
# INITIATE SESSION
session["filename"] = "Select file.."
plot_arguments = figure_defaults()
session["plot_arguments"] = plot_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "david"
if request.method == 'POST':
try:
if request.files["inputsessionfile"]:
msg, plot_arguments, error = read_session_file(
request.files["inputsessionfile"], "david")
if error:
flash(msg, 'error')
return render_template('/apps/david.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
if request.files["inputargumentsfile"]:
msg, plot_arguments, error = read_argument_file(
request.files["inputargumentsfile"], "david")
if error:
flash(msg, 'error')
return render_template('/apps/david.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
if not request.files["inputsessionfile"] and not request.files[
"inputargumentsfile"]:
plot_arguments = read_request(request)
if plot_arguments["user"] == "":
flash(
'Please give in a register DAVID email in "Input" > "DAVID registered email". If you do not yet have a registered address you need to register with DAVID - https://david.ncifcrf.gov/webservice/register.htm. Please be aware that you will not receive any confirmation email. ',
'error')
return render_template('/apps/david.html',
apps=apps,
**plot_arguments)
# CALL FIGURE FUNCTION
david_df, report_stats, msg = run_david(plot_arguments)
if msg:
flash(msg, "error")
return render_template('/apps/david.html',
apps=apps,
**plot_arguments)
# if (not david_df) and (not report_stats):
# flash("DAVID doesn't seem to recognize your email account. Make sure you have registered your account on https://david.ncifcrf.gov/webservice/register.htm. If you have just registered please be aware that it might take some hours for you account to be in their systems. Please try again later.",'error')
# return render_template('/apps/david.html', apps=apps, **plot_arguments)
## get this into json like in former apps
david_df = david_df.astype(str)
report_stats = report_stats.astype(str)
# mapped=mapped.astype(str)
session["david_df"] = david_df.to_json()
session["report_stats"] = report_stats.to_json()
# session["mapped"]=mapped.to_json()
table_headers = david_df.columns.tolist()
tmp = david_df[:50]
for col in ["%", "Fold Enrichment"]:
tmp[col] = tmp[col].apply(lambda x: "{0:.2f}".format(float(x)))
for col in ["PValue", "Bonferroni", "Benjamini", "FDR"]:
tmp[col] = tmp[col].apply(lambda x: '{:.2e}'.format(float(x)))
for col in ["Genes"] + table_headers[13:]:
tmp[col] = tmp[col].apply(lambda x: str(x)[:40] + "..")
david_contents = []
for i in tmp.index.tolist():
david_contents.append(list(tmp.loc[i, ]))
# david_in_store
if len(david_df) > 0:
session["david_in_store"] = True
return render_template('/apps/david.html',
david_in_store=True,
apps=apps,
table_headers=table_headers,
david_contents=david_contents,
**plot_arguments)
elif "david_in_store" in list(session.keys()):
del (session["david_in_store"])
return render_template('/apps/david.html',
apps=apps,
table_headers=table_headers,
david_contents=david_contents,
**plot_arguments)
except Exception as e:
tb_str = handle_exception(e,
user=current_user,
eapp="david",
session=session)
flash(tb_str, 'traceback')
if "david_in_store" in list(session.keys()):
del (session["david_in_store"])
return render_template('/apps/david.html',
apps=apps,
**plot_arguments)
else:
if download == "download":
plot_arguments = session["plot_arguments"]
# READ INPUT DATA FROM SESSION JSON
try:
david_df = pd.read_json(session["david_df"])
report_stats = pd.read_json(session["report_stats"])
except:
flash("No DAVID table in memory.", 'error')
return render_template('/apps/david.html',
apps=apps,
**plot_arguments)
# mapped=pd.read_json(session["mapped"])
# mapped=mapped.replace("nan",np.nan)
eventlog = UserLogging(email=current_user.email,
action="download david")
db.session.add(eventlog)
db.session.commit()
if plot_arguments["download_format_value"] == "xlsx":
def getGOID(x):
if "GO:" in x:
r = x.split("~")[0]
else:
r = np.nan
return r
revigo = david_df[["Term", "PValue"]]
revigo["Term"] = revigo["Term"].apply(lambda x: getGOID(x))
revigo = revigo.dropna()
outfile = io.BytesIO()
EXC = pd.ExcelWriter(outfile)
david_df.to_excel(EXC, sheet_name="david", index=None)
report_stats.to_excel(EXC, sheet_name="stats", index=None)
revigo.to_excel(EXC, sheet_name="revigo", index=None)
# mapped.to_excel(EXC,sheet_name="mapped",index=None)
EXC.save()
outfile.seek(0)
return send_file(
outfile,
attachment_filename=plot_arguments["download_name"] + "." +
plot_arguments["download_format_value"],
as_attachment=True)
elif plot_arguments["download_format_value"] == "tsv":
return Response(david_df.to_csv(sep="\t"),
mimetype="text/csv",
headers={
"Content-disposition":
"attachment; filename=%s.tsv" %
plot_arguments["download_name"]
})
#outfile.seek(0)
if download == "cellplot":
# READ INPUT DATA FROM SESSION JSON
david_df = pd.read_json(session["david_df"])
david_df = david_df.astype(str)
reset_info = check_session_app(session, "icellplot", apps)
if reset_info:
flash(reset_info, 'error')
# INITIATE SESSION
session["filename"] = "<from DAVID>"
session["ge_filename"] = "Select file.."
plot_arguments = icellplot.figure_defaults()
session["plot_arguments"] = plot_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "icellplot"
david_df = david_df.astype(str)
session["df"] = david_df.to_json()
cols = david_df.columns.tolist()
session["plot_arguments"]["david_cols"] = ["select a column.."
] + cols
session["plot_arguments"]["annotation_column"] = ["none"] + cols
session["plot_arguments"]["categories_to_plot"] = list(
set(david_df["Category"].tolist()))
session["plot_arguments"]["categories_to_plot_value"] = list(
set(david_df["Category"].tolist()))
return render_template('/apps/icellplot.html',
filename=session["filename"],
ge_filename=session["ge_filename"],
apps=apps,
**plot_arguments)
return render_template('apps/david.html',
apps=apps,
**session["plot_arguments"])
def icellplot(download=None):
"""
renders the plot on the fly.
https://gist.github.com/illume/1f19a2cf9f26425b1761b63d9506331f
"""
apps = current_user.user_apps
plot_arguments = None
reset_info = check_session_app(session, "icellplot", apps)
if reset_info:
flash(reset_info, 'error')
# INITIATE SESSION
session["filename"] = "Select file.."
session["ge_filename"] = "Select file.."
plot_arguments = figure_defaults()
session["plot_arguments"] = plot_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "icellplot"
if request.method == 'POST':
try:
if request.files["inputsessionfile"]:
msg, plot_arguments, error = read_session_file(
request.files["inputsessionfile"], "icellplot")
if error:
flash(msg, 'error')
return render_template('/apps/icellplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
if request.files["inputargumentsfile"]:
msg, plot_arguments, error = read_argument_file(
request.files["inputargumentsfile"], "icellplot")
if error:
flash(msg, 'error')
return render_template('/apps/icellplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
if not request.files["inputsessionfile"] and not request.files[
"inputargumentsfile"]:
plot_arguments = read_request(request)
missing_args = False
# IF THE UPLOADS A NEW FILE
# THAN UPDATE THE SESSION FILE
# READ INPUT FILE
inputfile = request.files["inputfile"]
if inputfile:
filename = secure_filename(inputfile.filename)
if allowed_file(inputfile.filename):
df = read_tables(inputfile)
cols = df.columns.tolist()
session["plot_arguments"]["david_cols"] = [
"select a column.."
] + cols
session["plot_arguments"]["annotation_column"] = ["none"
] + cols
# IF THE USER HAS NOT YET CHOSEN X AND Y VALUES THAN PLEASE SELECT
if (session["plot_arguments"]["terms_column"] not in cols
) | (session["plot_arguments"]["terms_column"]
== "select a column.."):
session["plot_arguments"][
"terms_column"] = "select a column.."
missing_args = True
if (session["plot_arguments"]["categories_column"]
not in cols) | (
session["plot_arguments"]["categories_column"]
== "select a column.."):
session["plot_arguments"][
"categories_column"] = "select a column.."
missing_args = True
else:
session["plot_arguments"]["categories_to_plot"] = list(
set(df[session["plot_arguments"]
["categories_column"]].tolist()))
session["plot_arguments"][
"categories_to_plot_value"] = list(
set(df[session["plot_arguments"]
["categories_column"]].tolist()))
if (session["plot_arguments"]["david_gene_ids"] not in cols
) | (session["plot_arguments"]["david_gene_ids"]
== "select a column.."):
session["plot_arguments"][
"david_gene_ids"] = "select a column.."
missing_args = True
if (session["plot_arguments"]["plotvalue"] not in cols) | (
session["plot_arguments"]["plotvalue"]
== "select a column.."):
session["plot_arguments"][
"plotvalue"] = "select a column.."
missing_args = True
if missing_args:
sometext = "Please select matching columns from DAVID file."
flash(sometext, 'info')
else:
# IF UPLOADED FILE DOES NOT CONTAIN A VALID EXTENSION PLEASE UPDATE
error_message = "You can can only upload files with the following extensions: 'xlsx', 'tsv', 'csv'. Please make sure the file '%s' \
has the correct format and respective extension and try uploadling DAVID's output again." % filename
flash(error_msg, 'error')
session["filename"] = "Select file.."
annotation_columns = (
session["plot_arguments"]["annotation_column_value"] != "none"
) & (session["plot_arguments"]["annotation2_column_value"] !=
"none")
if (not annotation_columns):
ge_inputfile = request.files["ge_inputfile"]
if ge_inputfile:
filename = secure_filename(ge_inputfile.filename)
if allowed_file(ge_inputfile.filename):
df = read_tables(ge_inputfile,
session_key="ge_df",
file_field="ge_filename")
cols = df.columns.tolist()
session["plot_arguments"]["ge_cols"] = [
"select a column.."
] + cols
# IF THE USER HAS NOT YET CHOSEN X AND Y VALUES THAN PLEASE SELECT
if (session["plot_arguments"]["gene_identifier"]
not in cols
) | (session["plot_arguments"]["gene_identifier"]
== "select a column.."):
session["plot_arguments"][
"gene_identifier"] = "select a column.."
missing_args = True
if (session["plot_arguments"]["expression_values"]
not in cols
) | (session["plot_arguments"]["expression_values"]
== "select a column.."):
session["plot_arguments"][
"expression_values"] = "select a column.."
missing_args = True
if (session["plot_arguments"]["gene_name"] not in cols
) | (session["plot_arguments"]["gene_name"]
== "select a column.."):
session["plot_arguments"][
"gene_name"] = "select a column.."
missing_args = True
if missing_args:
sometext = "Please select matching columns in gene expression file for mapping."
flash(sometext, 'info')
else:
# IF UPLOADED FILE DOES NOT CONTAIN A VALID EXTENSION PLEASE UPDATE
error_message = "You can can only upload files with the following extensions: 'xlsx', 'tsv', 'csv'. Please make sure the file '%s' \
has the correct format and respective extension and try uploadling the gene expression file again." % filename
flash(error_message, 'error')
session["ge_filename"] = "Select file.."
if ((session["ge_filename"] == "Select file..") &
(not annotation_columns)) | (session["filename"]
== "Select file.."):
plot_arguments = session["plot_arguments"]
return render_template('/apps/icellplot.html',
filename=session["filename"],
ge_filename=session["ge_filename"],
apps=apps,
**plot_arguments)
if missing_args:
plot_arguments = session["plot_arguments"]
return render_template('/apps/icellplot.html',
filename=session["filename"],
ge_filename=session["ge_filename"],
apps=apps,
**plot_arguments)
annotation_columns = (
session["plot_arguments"]["annotation_column_value"] != "none"
) & (session["plot_arguments"]["annotation2_column_value"] !=
"none")
if ("df" not in list(
session.keys())) | (("ge_df" not in list(session.keys())) &
(not annotation_columns)):
error_message = "No data to plot, please upload a data or session file."
flash(error_msg, 'error')
return render_template('/apps/icellplot.html',
filename=session["filename"],
ge_filename=session["ge_filename"],
apps=apps,
**plot_arguments)
# MAKE SURE WE HAVE THE LATEST ARGUMENTS FOR THIS SESSION
plot_arguments = session["plot_arguments"]
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
if (annotation_columns) & ("ge_df" not in list(session.keys())):
ge_df = pd.DataFrame()
session["ge_df"] = ge_df.to_json()
ge_df = pd.read_json(session["ge_df"])
# CALL FIGURE FUNCTION
# try:
fig = make_figure(df, ge_df, plot_arguments)
figure_url = json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)
return render_template('/apps/icellplot.html',
figure_url=figure_url,
filename=session["filename"],
ge_filename=session["ge_filename"],
apps=apps,
**plot_arguments)
except Exception as e:
tb_str = handle_exception(e,
user=current_user,
eapp="icellplot",
session=session)
flash(tb_str, 'traceback')
if not plot_arguments:
plot_arguments = session["plot_arguments"]
return render_template('/apps/icellplot.html',
filename=session["filename"],
ge_filename=session["ge_filename"],
apps=apps,
**plot_arguments)
else:
if download == "download":
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
ge_df = pd.read_json(session["ge_df"])
plot_arguments = session["plot_arguments"]
# CALL FIGURE FUNCTION
fig = make_figure(df, ge_df, plot_arguments)
pio.orca.config.executable = '/miniconda/bin/orca'
pio.orca.config.use_xvfb = True
#pio.orca.config.save()
figfile = io.BytesIO()
mimetypes = {
"png": 'image/png',
"pdf": "application/pdf",
"svg": "image/svg+xml"
}
pa_ = {}
for v in ["height", "width"]:
if plot_arguments[v] != "":
pa_[v] = None
elif plot_arguments[v]:
pa_[v] = float(plot_arguments[v])
else:
pa_[v] = None
if pa_["height"]:
if pa_["width"]:
fig.write_image(figfile,
format=plot_arguments["downloadf"],
height=pa_["height"],
width=pa_["width"])
else:
fig.write_image(figfile,
format=plot_arguments["downloadf"])
else:
fig.write_image(figfile, format=plot_arguments["downloadf"])
figfile.seek(0) # rewind to beginning of file
eventlog = UserLogging(email=current_user.email,
action="download figure icellplot")
db.session.add(eventlog)
db.session.commit()
return send_file(figfile,
mimetype=mimetypes[plot_arguments["downloadf"]],
as_attachment=True,
attachment_filename=plot_arguments["downloadn"] +
"." + plot_arguments["downloadf"])
return render_template('apps/icellplot.html',
filename=session["filename"],
ge_filename=session["ge_filename"],
apps=apps,
**session["plot_arguments"])
def igseaplot(download=None):
"""
renders the plot on the fly.
https://gist.github.com/illume/1f19a2cf9f26425b1761b63d9506331f
"""
apps = current_user.user_apps
plot_arguments = None
reset_info = check_session_app(session, "igseaplot", apps)
if reset_info:
flash(reset_info, 'error')
# INITIATE SESSION
session["filename"] = "Select file.."
plot_arguments = figure_defaults()
session["plot_arguments"] = plot_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "igseaplot"
if request.method == 'POST':
try:
# READ SESSION FILE IF AVAILABLE
# AND OVERWRITE VARIABLES
if request.files["inputsessionfile"]:
msg, plot_arguments, error = read_session_file(
request.files["inputsessionfile"], "igseaplot")
if error:
flash(msg, 'error')
return render_template('/apps/igseaplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
if request.files["inputargumentsfile"]:
msg, plot_arguments, error = read_argument_file(
request.files["inputargumentsfile"], "igseaplot")
if error:
flash(msg, 'error')
return render_template('/apps/igseaplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
flash(msg, "info")
# IF THE UPLOADS A NEW FILE
# THAN UPDATE THE SESSION FILE
# READ INPUT FILE
inputfile = request.files["inputfile"]
if inputfile:
filename = secure_filename(inputfile.filename)
if allowed_file(inputfile.filename):
df = read_tables(inputfile)
cols = df.columns.tolist()
if len(cols) < 2:
error_msg = "Your table needs to have at least 2 columns. One for the x- and one for the y-value."
flash(error_msg, 'error')
return render_template('/apps/igseaplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
if session["plot_arguments"]["groups"] not in cols:
session["plot_arguments"]["groups"] = ["None"] + cols
columns_select=["markerstyles_cols", "markerc_cols", "markersizes_cols","markeralpha_col",\
"labels_col","gseacolor_cols","gsea_linewidth_cols",]
for parg in columns_select:
if session["plot_arguments"][
"markerstyles_cols"] not in cols:
session["plot_arguments"][parg] = [
"select a column.."
] + cols
session["plot_arguments"]["xcols"] = cols
session["plot_arguments"]["ycols"] = cols
# IF THE USER HAS NOT YET CHOOSEN X AND Y VALUES THAN PLEASE SELECT
if (session["plot_arguments"]["xvals"] not in cols) | (
session["plot_arguments"]["yvals"] not in cols):
session["plot_arguments"]["xvals"] = cols[0]
session["plot_arguments"]["yvals"] = cols[1]
sometext = "Please select which values should map to the x and y axes."
plot_arguments = session["plot_arguments"]
flash(sometext, 'info')
return render_template('/apps/igseaplot.html',
filename=filename,
apps=apps,
**plot_arguments)
plot_arguments = session["plot_arguments"]
flash("New file uploaded.", 'info')
return render_template('/apps/igseaplot.html',
filename=filename,
apps=apps,
**plot_arguments)
else:
# IF UPLOADED FILE DOES NOT CONTAIN A VALID EXTENSION PLEASE UPDATE
error_msg = "You can can only upload files with the following extensions: 'xlsx', 'tsv', 'csv'. Please make sure the file '%s' \
has the correct format and respective extension and try uploadling it again." % filename
flash(error_msg, 'error')
return render_template('/apps/igseaplot.html',
filename="Select file..",
apps=apps,
**plot_arguments)
if not request.files["inputsessionfile"] and not request.files[
"inputargumentsfile"]:
# SELECTION LISTS DO NOT GET UPDATED
# lists=session["lists"]
# USER INPUT/PLOT_ARGUMENTS GETS UPDATED TO THE LATEST INPUT
# WITH THE EXCEPTION OF SELECTION LISTS
plot_arguments = session["plot_arguments"]
# if request.form["groups_value"] == "None":
# plot_arguments["groups_value"]="None"
if plot_arguments["groups_value"] != request.form[
"groups_value"]:
if request.form["groups_value"] != "None":
df = pd.read_json(session["df"])
df[request.form["groups_value"]] = df[
request.form["groups_value"]].apply(
lambda x: secure_filename(str(x)))
df = df.astype(str)
session["df"] = df.to_json()
groups = df[request.form["groups_value"]]
groups = list(set(groups))
groups.sort()
plot_arguments["list_of_groups"] = groups
groups_settings = []
group_dic = {}
for group in groups:
group_dic={"name":group,\
"markers":plot_arguments["markers"],\
"markersizes_col":"select a column..",\
"markerc":random.choice([ cc for cc in plot_arguments["marker_color"] if cc != "white"]),\
"markerc_col":"select a column..",\
"markerc_write":plot_arguments["markerc_write"],\
"gsea_linewidth":plot_arguments["gsea_linewidth"],\
"gsea_linewidth_col":"select a column..",\
"gseacolor":plot_arguments["gseacolor"],\
"gseacolor_col":"select a column..",\
"gseacolor_write":"",\
"marker":random.choice(plot_arguments["markerstyles"]),\
"markerstyles_col":"select a column..",\
"marker_alpha":plot_arguments["marker_alpha"],\
"markeralpha_col_value":"select a column.."}
groups_settings.append(group_dic)
plot_arguments["groups_settings"] = groups_settings
elif request.form["groups_value"] == "None":
plot_arguments["groups_settings"] = []
plot_arguments["list_of_groups"] = []
elif plot_arguments["groups_value"] != "None":
groups_settings = []
group_dic = {}
for group in plot_arguments["list_of_groups"]:
group_dic={"name":group,\
"markers":request.form["%s.markers" %group],\
"markersizes_col":request.form["%s.markersizes_col" %group],\
"markerc":request.form["%s.markerc" %group],\
"markerc_col":request.form["%s.markerc_col" %group],\
"markerc_write":request.form["%s.markerc_write" %group],\
"gsea_linewidth":request.form["%s.gsea_linewidth" %group],\
"gsea_linewidth_col":request.form["%s.gsea_linewidth_col" %group],\
"gseacolor":request.form["%s.gseacolor" %group],\
"gseacolor_col":request.form["%s.gseacolor_col" %group],\
"gseacolor_write":request.form["%s.gseacolor_write" %group],\
"centerline":request.form["%s.centerline" %group],\
"marker":request.form["%s.marker" %group],\
"markerstyles_col":request.form["%s.markerstyles_col" %group],\
"marker_alpha":request.form["%s.marker_alpha" %group],\
"markeralpha_col_value":request.form["%s.markeralpha_col_value" %group]
}
groups_settings.append(group_dic)
plot_arguments["groups_settings"] = groups_settings
if request.form["labels_col_value"] != "select a column..":
df = pd.read_json(session["df"])
plot_arguments["available_labels"] = list(
set(df[request.form["labels_col_value"]].tolist()))
session["plot_arguments"] = plot_arguments
plot_arguments = read_request(request)
if "df" not in list(session.keys()):
error_msg = "No data to plot, please upload a data or session file."
flash(error_msg, 'error')
return render_template('/apps/igseaplot.html',
filename="Select file..",
apps=apps,
**plot_arguments)
# MAKE SURE WE HAVE THE LATEST ARGUMENTS FOR THIS SESSION
filename = session["filename"]
plot_arguments = session["plot_arguments"]
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
#CALL FIGURE FUNCTION
fig = make_figure(df, plot_arguments)
figure_url = json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)
return render_template('/apps/igseaplot.html',
figure_url=figure_url,
filename=filename,
apps=apps,
**plot_arguments)
except Exception as e:
tb_str = handle_exception(e,
user=current_user,
eapp="igseaplot",
session=session)
flash(tb_str, 'traceback')
if not plot_arguments:
plot_arguments = session["plot_arguments"]
filename = session["filename"]
return render_template('/apps/igseaplot.html',
filename=filename,
apps=apps,
**plot_arguments)
else:
if download == "download":
# READ INPUT DATA FROM SESSION JSON
df = pd.read_json(session["df"])
plot_arguments = session["plot_arguments"]
# CALL FIGURE FUNCTION
fig = make_figure(df, plot_arguments)
pio.orca.config.executable = '/miniconda/bin/orca'
pio.orca.config.use_xvfb = True
#pio.orca.config.save()
figfile = io.BytesIO()
mimetypes = {
"png": 'image/png',
"pdf": "application/pdf",
"svg": "image/svg+xml"
}
pa_ = {}
for v in ["fig_height", "fig_width"]:
if plot_arguments[v] != "":
pa_[v] = False
elif plot_arguments[v]:
pa_[v] = float(plot_arguments[v])
else:
pa_[v] = False
if (pa_["fig_height"]) & (pa_["fig_width"]):
fig.write_image(figfile,
format=plot_arguments["downloadf"],
height=pa_["fig_height"],
width=pa_["fig_width"])
else:
fig.write_image(figfile, format=plot_arguments["downloadf"])
figfile.seek(0) # rewind to beginning of file
eventlog = UserLogging(email=current_user.email,
action="download figure igseaplot")
db.session.add(eventlog)
db.session.commit()
return send_file(figfile,
mimetype=mimetypes[plot_arguments["downloadf"]],
as_attachment=True,
attachment_filename=plot_arguments["downloadn"] +
"." + plot_arguments["downloadf"])
return render_template('apps/igseaplot.html',
filename=session["filename"],
apps=apps,
**session["plot_arguments"])
def kegg(download=None):
apps=current_user.user_apps
# pa={}
# pa["ids"]="HMDB00001\tred\nHMDB0004935\tred"
# pa["species"]="mmu"
# make_figure(pa)
# return render_template('/index.html' ,apps=apps)
reset_info=check_session_app(session,"kegg",apps)
if reset_info:
flash(reset_info,'error')
# INITIATE SESSION
plot_arguments=figure_defaults()
print(plot_arguments)
session["plot_arguments"]=plot_arguments
session["COMMIT"]=app.config['COMMIT']
session["app"]="kegg"
if request.method == 'POST' :
try:
if request.files["inputsessionfile"] :
msg, plot_arguments, error=read_session_file(request.files["inputsessionfile"],"kegg")
if error:
flash(msg,'error')
return render_template('/apps/kegg.html' ,apps=apps, **plot_arguments)
flash(msg,"info")
if request.files["inputargumentsfile"] :
msg, plot_arguments, error=read_argument_file(request.files["inputargumentsfile"],"kegg")
if error:
flash(msg,'error')
return render_template('/apps/kegg.html' , apps=apps, **plot_arguments)
flash(msg,"info")
if not request.files["inputsessionfile"] and not request.files["inputargumentsfile"] :
plot_arguments=read_request(request)
# CALL FIGURE FUNCTION
df, msg=make_figure(plot_arguments)
## get this into json like in former apps
df=df.astype(str)
# mapped=mapped.astype(str)
session["df"]=df.to_json()
# session["mapped"]=mapped.to_json()
# print(df.head())
tmp=df[:50]
table_headers=tmp.columns.tolist()
def break_text(s,w=20):
r=[s[i:i + w] for i in range(0, len(s), w)]
r="".join(r)
return r
for c in ["ref_link","species_link"]:
tmp[c]=tmp[c].apply(lambda x: break_text(x) )
kegg_contents=[]
for i in tmp.index.tolist():
kegg_contents.append(list(tmp.loc[i,]))
#print(kegg_contents[:2])
# david_in_store
if len(df)>0:
session["kegg_in_store"]=True
return render_template('/apps/kegg.html', kegg_in_store=True, apps=apps, table_headers=table_headers, kegg_contents=kegg_contents, **plot_arguments)
elif "kegg_in_store" in list(session.keys()):
del(session["kegg_in_store"])
return render_template('/apps/kegg.html', apps=apps, table_headers=table_headers, kegg_contents=kegg_contents, **plot_arguments)
except Exception as e:
tb_str=handle_exception(e,user=current_user,eapp="kegg",session=session)
flash(tb_str,'traceback')
if "kegg_in_store" in list(session.keys()):
del(session["kegg_in_store"])
return render_template('/apps/kegg.html', apps=apps, **plot_arguments)
else:
if download == "download":
plot_arguments=session["plot_arguments"]
# READ INPUT DATA FROM SESSION JSON
df=pd.read_json(session["df"])
# mapped=pd.read_json(session["mapped"])
# mapped=mapped.replace("nan",np.nan)
eventlog = UserLogging(email=current_user.email,action="download kegg")
db.session.add(eventlog)
db.session.commit()
if plot_arguments["download_format_value"] == "xlsx":
outfile = io.BytesIO()
EXC=pd.ExcelWriter(outfile)
df.to_excel(EXC,sheet_name="kegg",index=None)
# mapped.to_excel(EXC,sheet_name="mapped",index=None)
EXC.save()
outfile.seek(0)
return send_file(outfile, attachment_filename=plot_arguments["download_name"]+ "." + plot_arguments["download_format_value"],as_attachment=True )
elif plot_arguments["download_format_value"] == "tsv":
return Response(df.to_csv(sep="\t"), mimetype="text/csv", headers={"Content-disposition": "attachment; filename=%s.tsv" %plot_arguments["download_name"]})
#outfile.seek(0)
return render_template('apps/kegg.html', apps=apps, **session["plot_arguments"])
def submissions():
apps = current_user.user_apps
reset_info = check_session_app(session, "submissions", apps)
if reset_info:
flash(reset_info, 'error')
# INITIATE SESSION
session["filename"] = "Select file.."
# submission_arguments=submission_defaults()
# session["plot_arguments"]=submission_arguments
session["COMMIT"] = app.config['COMMIT']
session["app"] = "submissions"
if request.method == 'POST':
try:
# if request.files["inputsessionfile"] :
# msg, plot_arguments, error=read_session_file(request.files["inputsessionfile"],"submissions")
# if error:
# flash(msg,'error')
# return render_template('/apps/submissions.html' , filename=session["filename"],apps=apps, **plot_arguments)
# flash(msg,"info")
# if request.files["inputargumentsfile"] :
# msg, plot_arguments, error=read_argument_file(request.files["inputargumentsfile"],"david")
# if error:
# flash(msg,'error')
# return render_template('/apps/submissions.html' , filename=session["filename"], apps=apps, **plot_arguments)
# flash(msg,"info")
# if not request.files["inputsessionfile"] and not request.files["inputargumentsfile"] :
# plot_arguments=read_request(request)
inputfile = request.files["inputfile"]
if inputfile:
filename = secure_filename(inputfile.filename)
if not allowed_file(inputfile.filename):
msg = "This file is not allowed."
flash(msg, "error")
return render_template('/apps/submissions.html', apps=apps)
# CALL FIGURE FUNCTION
status, msg, attachment_path = submission_check(inputfile)
if not status:
flash(msg, "error")
return render_template('/apps/submissions.html',
apps=apps) #, **plot_arguments)
if status:
flash(msg)
send_submission_email(user=current_user,
submission_type=status,
submission_file=inputfile,
attachment_path=attachment_path)
return render_template('/apps/submissions.html',
apps=apps) #, **plot_arguments)
# return render_template('/apps/submissions.html', apps=apps, **plot_arguments)
except Exception as e:
tb_str = handle_exception(e,
user=current_user,
eapp="submissions",
session=session)
flash(tb_str, 'traceback')
return render_template('/apps/submissions.html',
apps=apps) #, **plot_arguments)
else:
initial_message = Markup(
'For submitting samples please follow the instructions in <a href="https://github.com/mpg-age-bioinformatics/submissions/blob/main/README.md#submissions" class="alert-link">here</a>.'
)
flash(initial_message)
return render_template('apps/submissions.html',
apps=apps) #, **session["plot_arguments"])
def scatterplot(download=None):
apps=current_user.user_apps
reset_info=check_session_app(session,"scatterplot",apps)
if reset_info:
flash(reset_info,'error')
# INITIATE SESSION
session["filename"]="Select file.."
plot_arguments=figure_defaults()
session["plot_arguments"]=plot_arguments
session["COMMIT"]=app.config['COMMIT']
session["app"]="scatterplot"
if request.method == 'POST' :
try:
if request.files["inputsessionfile"] :
msg, plot_arguments, error=read_session_file(request.files["inputsessionfile"],"scatterplot")
if error:
flash(msg,'error')
return render_template('/apps/scatterplot.html' , filename=session["filename"],apps=apps, **plot_arguments)
flash(msg,"info")
if request.files["inputargumentsfile"] :
msg, plot_arguments, error=read_argument_file(request.files["inputargumentsfile"],"scatterplot")
if error:
flash(msg,'error')
return render_template('/apps/scatterplot.html' , filename=session["filename"], apps=apps, **plot_arguments)
flash(msg,"info")
# IF THE UPLOADS A NEW FILE
# THAN UPDATE THE SESSION FILE
# READ INPUT FILE
inputfile = request.files["inputfile"]
if inputfile:
filename = secure_filename(inputfile.filename)
if allowed_file(inputfile.filename):
df=read_tables(inputfile)
cols=df.columns.tolist()
if len(cols) < 2 :
error_msg="Your table needs to have at least 2 columns. One for the x- and one for the y-value."
flash(error_msg,'error')
return render_template('/apps/scatterplot.html' , filename=session["filename"], apps=apps, **plot_arguments)
session["filename"]=filename
if session["plot_arguments"]["groups"] not in cols:
session["plot_arguments"]["groups"]=["None"]+cols
columns_select=["markerstyles_cols", "markerc_cols", "markersizes_cols","markeralpha_col",\
"labels_col","edgecolor_cols","edge_linewidth_cols"]
for parg in columns_select:
if session["plot_arguments"]["markerstyles_cols"] not in cols:
session["plot_arguments"][parg]=["select a column.."]+cols
session["plot_arguments"]["xcols"]=cols
session["plot_arguments"]["ycols"]=cols
# IF THE USER HAS NOT YET CHOOSEN X AND Y VALUES THAN PLEASE SELECT
if (session["plot_arguments"]["xvals"] not in cols) | (session["plot_arguments"]["yvals"] not in cols):
if session["plot_arguments"]["xvals"] not in cols :
session["plot_arguments"]["xvals"]=cols[0]
if session["plot_arguments"]["yvals"] not in cols:
session["plot_arguments"]["yvals"]=cols[1]
sometext="Please select which values should map to the x and y axes."
plot_arguments=session["plot_arguments"]
flash(sometext,'info')
return render_template('/apps/scatterplot.html' , filename=filename, apps=apps,**plot_arguments)
plot_arguments=session["plot_arguments"]
flash("New file uploaded.",'info')
return render_template('/apps/scatterplot.html' , filename=filename, apps=apps,**plot_arguments)
else:
plot_arguments=session["plot_arguments"]
# IF UPLOADED FILE DOES NOT CONTAIN A VALID EXTENSION PLEASE UPDATE
error_msg="You can can only upload files with the following extensions: 'xlsx', 'tsv', 'csv'. Please make sure the file '%s' \
has the correct format and respective extension and try uploadling it again." %filename
flash(error_msg,'error')
return render_template('/apps/scatterplot.html' , filename=session["filename"], apps=apps, **plot_arguments)
if not request.files["inputsessionfile"] and not request.files["inputargumentsfile"] :
# USER INPUT/PLOT_ARGUMENTS GETS UPDATED TO THE LATEST INPUT
# WITH THE EXCEPTION OF SELECTION LISTS
plot_arguments = session["plot_arguments"]
# if request.form["groups_value"] == "None":
# plot_arguments["groups_value"]="None"
if plot_arguments["groups_value"]!=request.form["groups_value"] :
if request.form["groups_value"] != "None":
df=pd.read_json(session["df"])
df[request.form["groups_value"]]=df[request.form["groups_value"]].apply(lambda x: secure_filename(str(x) ) )
df=df.astype(str)
session["df"]=df.to_json()
groups=df[request.form["groups_value"]]
groups=list(set(groups))
groups.sort()
plot_arguments["list_of_groups"]=groups
groups_settings=[]
for group in groups:
group_dic={"name":group,\
"markers":plot_arguments["markers"],\
"markersizes_col":"select a column..",\
"markerc":random.choice([ cc for cc in plot_arguments["marker_color"] if cc != "white"]),\
"markerc_col":"select a column..",\
"markerc_write":plot_arguments["markerc_write"],\
"edge_linewidth":plot_arguments["edge_linewidth"],\
"edge_linewidth_col":"select a column..",\
"edgecolor":plot_arguments["edgecolor"],\
"edgecolor_col":"select a column..",\
"edgecolor_write":"",\
"marker":random.choice(plot_arguments["markerstyles"]),\
"markerstyles_col":"select a column..",\
"marker_alpha":plot_arguments["marker_alpha"],\
"markeralpha_col_value":"select a column.."}
groups_settings.append(group_dic)
# for k in list( group_dic[group].keys() ):
# plot_arguments[k+"_"+group]=group_dic[group][k]
plot_arguments["groups_settings"]=groups_settings
else:
groups_settings=[]
elif plot_arguments["groups_value"] != "None":
groups_settings=[]
for group in plot_arguments["list_of_groups"]:
group_dic={"name":group,\
"markers":request.form["%s.markers" %group],\
"markersizes_col":request.form["%s.markersizes_col" %group],\
"markerc":request.form["%s.markerc" %group],\
"markerc_col":request.form["%s.markerc_col" %group],\
"markerc_write":request.form["%s.markerc_write" %group],\
"edge_linewidth":request.form["%s.edge_linewidth" %group],\
"edge_linewidth_col":request.form["%s.edge_linewidth_col" %group],\
"edgecolor":request.form["%s.edgecolor" %group],\
"edgecolor_col":request.form["%s.edgecolor_col" %group],\
"edgecolor_write":request.form["%s.edgecolor_write" %group],\
"marker":request.form["%s.marker" %group],\
"markerstyles_col":request.form["%s.markerstyles_col" %group],\
"marker_alpha":request.form["%s.marker_alpha" %group],\
"markeralpha_col_value":request.form["%s.markeralpha_col_value" %group]
}
groups_settings.append(group_dic)
plot_arguments["groups_settings"]=groups_settings
session["plot_arguments"]=plot_arguments
plot_arguments=read_request(request)
if "df" not in list(session.keys()):
error_msg="No data to plot, please upload a data or session file."
flash(error_msg,'error')
return render_template('/apps/scatterplot.html' , filename="Select file..", apps=apps, **plot_arguments)
# MAKE SURE WE HAVE THE LATEST ARGUMENTS FOR THIS SESSION
filename=session["filename"]
plot_arguments=session["plot_arguments"]
# READ INPUT DATA FROM SESSION JSON
df=pd.read_json(session["df"])
fig=make_figure(df,plot_arguments)
#TRANSFORM FIGURE TO BYTES AND BASE64 STRING
figfile = io.BytesIO()
plt.savefig(figfile, format='png')
plt.close()
figfile.seek(0) # rewind to beginning of file
figure_url = base64.b64encode(figfile.getvalue()).decode('utf-8')
return render_template('/apps/scatterplot.html', figure_url=figure_url, filename=filename, apps=apps, **plot_arguments)
except Exception as e:
tb_str=handle_exception(e,user=current_user,eapp="scatterplot",session=session)
flash(tb_str,'traceback')
return render_template('/apps/scatterplot.html', filename=session["filename"], apps=apps, **session["plot_arguments"])
else:
if download == "download":
# READ INPUT DATA FROM SESSION JSON
df=pd.read_json(session["df"])
plot_arguments=session["plot_arguments"]
# CALL FIGURE FUNCTION
fig=make_figure(df,plot_arguments)
figfile = io.BytesIO()
mimetypes={"png":'image/png',"pdf":"application/pdf","svg":"image/svg+xml"}
plt.savefig(figfile, format=plot_arguments["downloadf"])
plt.close()
figfile.seek(0) # rewind to beginning of file
eventlog = UserLogging(email=current_user.email,action="download figure scatterplot")
db.session.add(eventlog)
db.session.commit()
return send_file(figfile, mimetype=mimetypes[plot_arguments["downloadf"]], as_attachment=True, attachment_filename=plot_arguments["downloadn"]+"."+plot_arguments["downloadf"] )
return render_template('apps/scatterplot.html', filename=session["filename"], apps=apps, **session["plot_arguments"])
