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 iscatterplot(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, "iscatterplot", 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"] = "iscatterplot"
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"], "iscatterplot")
if error:
flash(msg, 'error')
return render_template('/apps/iscatterplot.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"], "iscatterplot")
if error:
flash(msg, 'error')
return render_template('/apps/iscatterplot.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/iscatterplot.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","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):
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/iscatterplot.html',
filename=filename,
apps=apps,
**plot_arguments)
plot_arguments = session["plot_arguments"]
flash("New file uploaded.", 'info')
return render_template('/apps/iscatterplot.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/iscatterplot.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"],\
"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)
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],\
"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
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/iscatterplot.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/iscatterplot.html',
figure_url=figure_url,
filename=filename,
apps=apps,
**plot_arguments)
except Exception as e:
tb_str = handle_exception(e,
user=current_user,
eapp="iscatterplot",
session=session)
flash(tb_str, 'traceback')
if not plot_arguments:
plot_arguments = session["plot_arguments"]
filename = session["filename"]
return render_template('/apps/iscatterplot.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 iscatterplot")
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/iscatterplot.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 iscatterplot(download=None):
"""
renders the plot on the fly.
https://gist.github.com/illume/1f19a2cf9f26425b1761b63d9506331f
"""
reset_info = check_session_app(session, "scatterplot", apps)
if reset_info:
flash(reset_info, 'error')
apps = FREEAPPS + session["PRIVATE_APPS"]
if request.method == 'POST':
# READ SESSION FILE IF AVAILABLE
# AND OVERWRITE VARIABLES
inputsessionfile = request.files["inputsessionfile"]
if inputsessionfile:
if inputsessionfile.filename.rsplit('.', 1)[1].lower() != "ses":
plot_arguments = session["plot_arguments"]
error_msg = "The file you have uploaded is not a session file. Please make sure you upload a session file with the correct `ses` extension."
flash(error_msg, 'error')
return render_template('/apps/iscatterplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
session_ = json.load(inputsessionfile)
if session_["ftype"] != "session":
plot_arguments = session["plot_arguments"]
error_msg = "The file you have uploaded is not a session file. Please make sure you upload a session file."
flash(error_msg, 'error')
return render_template('/apps/iscatterplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
if session_["app"] != "iscatterplot":
plot_arguments = session["plot_arguments"]
error_msg = "The file was not loaded as it is associated with the '%s' and not with this app." % session_[
"app"]
flash(error_msg, 'error')
return render_template('/apps/iscatterplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
del (session_["ftype"])
del (session_["COMMIT"])
for k in list(session_.keys()):
session[k] = session_[k]
plot_arguments = session["plot_arguments"]
flash('Session file sucessufuly read.')
# READ ARGUMENTS FILE IF AVAILABLE
# AND OVERWRITE VARIABLES
inputargumentsfile = request.files["inputargumentsfile"]
if inputargumentsfile:
if inputargumentsfile.filename.rsplit('.', 1)[1].lower() != "arg":
plot_arguments = session["plot_arguments"]
error_msg = "The file you have uploaded is not a arguments file. Please make sure you upload a session file with the correct `arg` extension."
flash(error_msg, 'error')
return render_template('/apps/iscatterplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
session_ = json.load(inputargumentsfile)
if session_["ftype"] != "arguments":
plot_arguments = session["plot_arguments"]
error_msg = "The file you have uploaded is not an arguments file. Please make sure you upload an arguments file."
flash(error_msg, 'error')
return render_template('/apps/iscatterplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
if session_["app"] != "iscatterplot":
plot_arguments = session["plot_arguments"]
error_msg = "The file was not load as it is associated with the '%s' and not with this app." % session_[
"app"]
flash(error_msg, 'error')
return render_template('/apps/iscatterplot.html',
filename=session["filename"],
apps=apps,
**plot_arguments)
del (session_["ftype"])
del (session_["COMMIT"])
for k in list(session_.keys()):
session[k] = session_[k]
plot_arguments = session["plot_arguments"]
flash('Arguments file sucessufuly read.', "info")
if not inputsessionfile and not 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"]
for a in list(plot_arguments.keys()):
if (a in list(request.form.keys())) & (a not in list(
lists.keys()) + session["notUpdateList"]):
plot_arguments[a] = request.form[a]
# # VALUES SELECTED FROM SELECTION LISTS
# # GET UPDATED TO THE LATEST CHOICE
# for k in list(lists.keys()):
# if k in list(request.form.keys()):
# plot_arguments[lists[k]]=request.form[k]
# checkboxes
for checkbox in session["checkboxes"]:
if checkbox in list(request.form.keys()):
plot_arguments[checkbox] = "on"
else:
try:
plot_arguments[checkbox] = request.form[checkbox]
except:
if plot_arguments[checkbox][0] != ".":
plot_arguments[checkbox] = "off"
# 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):
session["filename"] = filename
fileread = inputfile.read()
filestream = io.BytesIO(fileread)
extension = filename.rsplit('.', 1)[1].lower()
if extension == "xlsx":
df = pd.read_excel(filestream)
elif extension == "csv":
df = pd.read_csv(filestream)
elif extension == "tsv":
df = pd.read_csv(filestream, sep="\t")
df = df.astype(str)
session["df"] = df.to_json()
cols = df.columns.tolist()
if session["plot_arguments"]["groups"] not in cols:
session["plot_arguments"]["groups"] = ["None"] + cols
if session["plot_arguments"]["markerstyles_cols"] not in cols:
session["plot_arguments"]["markerstyles_cols"] = [
"select a column.."
] + cols
if session["plot_arguments"]["markerc_cols"] not in cols:
session["plot_arguments"]["markerc_cols"] = [
"select a column.."
] + cols
if session["plot_arguments"]["markersizes_cols"] not in cols:
session["plot_arguments"]["markersizes_cols"] = [
"select a column.."
] + cols
if session["plot_arguments"]["markeralpha_col"] not in cols:
session["plot_arguments"]["markeralpha_col"] = [
"select a column.."
] + cols
if session["plot_arguments"]["labels_col"] not in cols:
session["plot_arguments"]["labels_col"] = [
"select a column.."
] + 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"]["xcols"] = cols
session["plot_arguments"]["xvals"] = cols[0]
session["plot_arguments"]["ycols"] = 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/iscatterplot.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_msg, 'error')
return render_template('/apps/iscatterplot.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_msg, 'error')
return render_template('/apps/iscatterplot.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:
fig = make_figure(df, plot_arguments)
# TRANSFORM FIGURE TO HTML components
script, div = components(fig)
return render_template('/apps/iscatterplot.html',
the_script=script,
the_div=div,
filename=filename,
apps=apps,
**plot_arguments)
except Exception as e:
send_exception_email(user=current_user,
eapp="iscatterplot",
emsg=e,
etime=str(datetime.now()))
flash(e, 'error')
return render_template('/apps/iscatterplot.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)
# #flash('Figure is being sent to download but will not be updated on your screen.')
# figfile = io.BytesIO()
# figfile = io.StringIO()
# mimetypes={"png":'image/png',"pdf":"application/pdf","svg":"image/svg+xml"}
# if plot_arguments["downloadf"] == "svg":
# from bokeh.io import export_svgs
# export_svgs(fig, filename=fout)
# #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 iscatterplot")
# 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 "app" not in list(session.keys()):
return_to_plot = False
elif session["app"] != "iscatterplot":
return_to_plot = False
else:
return_to_plot = True
if not return_to_plot:
# INITIATE SESSION
session["filename"] = "Select file.."
plot_arguments, lists, notUpdateList, checkboxes = figure_defaults(
)
session["plot_arguments"] = plot_arguments
session["lists"] = lists
session["notUpdateList"] = notUpdateList
session["COMMIT"] = app.config['COMMIT']
session["app"] = "iscatterplot"
session["checkboxes"] = checkboxes
eventlog = UserLogging(email=current_user.email,
action="visit iscatterplot")
db.session.add(eventlog)
db.session.commit()
return render_template('apps/iscatterplot.html',
filename=session["filename"],
apps=apps,
**session["plot_arguments"])
# @app.route('/download/<json_type>', methods=['GET','POST'])
# @login_required
# def download(json_type="arg"):
# # READ INPUT DATA FROM SESSION JSON
# session_=session_to_file(session,json_type)
# session_file = io.BytesIO()
# session_file.write(json.dumps(session_).encode())
# session_file.seek(0)
# plot_arguments=session["plot_arguments"]
# eventlog = UserLogging(email=current_user.email,action="download %s iscatterplot" %json_type)
# db.session.add(eventlog)
# db.session.commit()
# return send_file(session_file, mimetype='application/json', as_attachment=True, attachment_filename=plot_arguments["session_argumentsn"]+"."+json_type )
