def group_list(colmun, mode, name, config):
import paplot.color as color
option_input = ""
if mode == "mutation":
option_input = "result_format_mutation"
elif mode == "ca":
option_input = "result_format_ca"
else:
return []
sept = tools.config_getstr(config, option_input, "sept_%s" % name)
limited_list = text_to_list(
tools.config_getstr(config, mode, "limited_%s" % name), ",")
nouse_list = text_to_list(
tools.config_getstr(config, mode, "nouse_%s" % name), ",")
funcs = []
for row in colmun:
splt = []
if sept == "": splt.append(row)
else: splt = row.split(sept)
for func in splt:
func = func.strip()
if func == "":
continue
if len(limited_list) > 0:
#if (func in limited_list) == False:
if fnmatch_list(func, limited_list) == False:
continue
#if func in nouse_list:
if fnmatch_list(func, nouse_list):
continue
funcs.append(func)
# sort list
funcs = list(set(funcs))
funcs.sort()
color_list = {}
for f in tools.config_getstr(config, mode, "%s_color" % name).split(","):
if len(f) == 0: continue
cols = text_to_list(f, ":")
if len(cols) >= 2:
color_list[cols[0]] = color.name_to_value(cols[1])
color_list = color.create_color_dict(funcs, color_list, color.metro_colors)
# dict to value
colors = []
for key in funcs:
colors.append(color_list[key])
return [funcs, colors]
def group_list(colmun, mode, name, config):
import paplot.color as color
option_input = ""
if mode == "mut":
option_input = "result_format_mutation"
elif mode == "sv":
option_input = "result_format_sv"
else:
return []
sept = tools.config_getstr(config, option_input, "sept_%s" % name)
limited_list = text_to_list(tools.config_getstr(config, mode, "limited_%ss" % name), ",")
nouse_list = text_to_list(tools.config_getstr(config, mode, "nouse_%ss" % name), ",")
funcs = []
for row in colmun:
splt = []
if sept == "": splt.append(row)
else: splt = row.split(sept)
for func in splt:
func = func.strip()
if func == "": continue
if len(limited_list) > 0:
if (func in limited_list) == False: continue
if func in nouse_list: continue
funcs.append(func)
# sort list
funcs = list(set(funcs))
funcs.sort()
color_n_list = {};
for f in tools.config_getstr(config, mode, "%s_colors" % name).split(","):
if len(f) == 0: continue
cols = text_to_list(f, ":")
if len(cols) >= 2:
color_n_list[cols[0]] = color.name_to_value(cols[1])
color_n_list = color.create_color_dict(funcs, color_n_list, color.metro_colors)
# dict to value
colors_n = []
for key in funcs:
colors_n.append(color_n_list[key])
return [funcs, colors_n]
def load_subdata(ids, sec, config):
import os
import paplot.subcode.tools as tools
import paplot.convert as convert
import paplot.color as color
input_file = tools.config_getpath(config, sec, "path", default = "")
if os.path.exists(input_file) == False:
print ("[ERROR] file is not exist. %s" % input_file)
return None
sept = tools.config_getstr(config, sec, "sept").replace("\\t", "\t").replace("\\n", "\n").replace("\\r", "\r")
mode = tools.config_getstr(config, sec, "mode")
comment = tools.config_getstr(config, sec, "comment")
title = tools.config_getstr(config, sec, "title")
label = []
item = []
colors_n_di = {}
colors_h_di = {}
for name_set in tools.config_getstr(config, sec, "name_set").split(","):
name_set_split = convert.text_to_list(name_set, ":")
for i in range(len(name_set_split)):
text = name_set_split[i]
if i == 0:
item.append(text)
if len(name_set_split) == 1:
label.append(text)
elif i == 1:
label.append(text)
elif i == 2:
colors_n_di[name_set_split[0]] = color.name_to_value(text)
elif i == 3:
colors_h_di[name_set_split[0]] = color.name_to_value(text)
# fill in undefined items
colors_n_di = color.create_color_dict(item, colors_n_di, color.osaka_subway_colors)
colors_h_di2 = {}
for key in colors_n_di:
if key in colors_h_di: continue
colors_h_di2[key] = color.saturation_down(colors_n_di[key])
# dict to value
colors_n = []
for key in item:
colors_n.append(colors_n_di[key])
if mode == "range":
item.remove(item[0])
header = []
if tools.config_getboolean(config, sec, "header") == True:
pos_value = -1
pos_id = -1
else:
pos_value = tools.config_getint(config, sec, "col_value")-1
pos_id = tools.config_getint(config, sec, "col_ID")-1
header = ["",""]
# copy id_list for find check
unlookup = []
for iid in ids:
unlookup.append(iid)
# read
data_text = ""
values = []
for line in open(input_file):
line = line.strip()
if len(line.replace(sept, "")) == 0:
continue
if comment != "" and line.find(comment) == 0:
continue
if len(header) == 0:
header = convert.text_to_list(line,sept)
try:
colname = tools.config_getstr(config, sec, "col_value")
pos_value = header.index(colname)
colname = tools.config_getstr(config, sec, "col_ID")
pos_id = header.index(colname)
except Exception as e:
print(e.message)
return None
continue
cols = convert.text_to_list(line,sept)
if (cols[pos_id] in ids) == False: continue
else: unlookup.remove(cols[pos_id])
id_pos = ids.index(cols[pos_id])
if mode == "fix":
if cols[pos_value] in item:
data_text += subdata_data_template.format(id = id_pos, item = item.index(cols[pos_value]))
else:
print("[" + sec + "] name_set: data is undefined." + cols[pos_value] + "\n")
continue
elif mode == "range" or mode == "gradient":
try:
values.append(float(cols[pos_value]))
except Exception as e:
print(colname + ": data type is invalid.\n" + e.message)
continue
data_text += subdata_data_template.format(id = id_pos, item = cols[pos_value])
if len(unlookup) > 0:
print("[WARNING] can't find IDs subplot data.")
print(unlookup)
if mode == "gradient" and len(values) > 0:
item[0] = min(values)
item[1] = max(values)
return [data_text, item, colors_n, label, title]
def convert_tojs(input_file, output_file, positions, config):
import os
import paplot.subcode.data_frame as data_frame
import paplot.subcode.merge as merge
import paplot.subcode.tools as tools
import paplot.convert as convert
import paplot.color as color
cols_di = merge.position_to_dict(positions)
# data read
try:
df = data_frame.load_file(input_file, header = 1, \
sept = tools.config_getstr(config, "result_format_qc", "sept"), \
comment = tools.config_getstr(config, "result_format_qc", "comment") \
)
except Exception as e:
print("failure open data %s, %s" % (input_file, e.message))
return None
if len(df.data) == 0:
print("no data %s" % input_file)
return None
# chart list
plots_text = ""
plots_option = []
config_sections = config.sections()
config_sections.sort()
if "qc_chart_brush" in config_sections:
config_sections.remove("qc_chart_brush")
config_sections.insert(0, "qc_chart_brush")
for sec in config.sections():
if not sec.startswith("qc_chart_"):
continue
chart_id = sec.replace("qc_chart_", "chart_")
stack_id = []
label = []
colors_di = {}
counter = 0
for name_set in tools.config_getstr(config, sec,
"name_set").split(","):
name_set_split = convert.text_to_list(name_set, ":")
if len(name_set_split) == 0:
continue
stack_id.append("stack" + str(counter))
label.append(name_set_split[0])
if len(name_set_split) > 1:
colors_di[name_set_split[0]] = color.name_to_value(
name_set_split[1])
counter += 1
# fill in undefined items
colors_di = color.create_color_dict(label, colors_di,
color.metro_colors)
# dict to value
colors_li = []
for key in label:
colors_li.append(colors_di[key])
plots_text += plot_template.format(
chart_id = chart_id, \
title = tools.config_getstr(config, sec, "title"), \
title_y = tools.config_getstr(config, sec, "title_y"), \
stack = convert.pyformat_to_jstooltip_text(cols_di, config, sec, "result_format_qc", "stack"), \
stack_id = convert.list_to_text(stack_id), \
label = convert.list_to_text(label), \
color = convert.list_to_text(colors_li), \
tooltip = convert.pyformat_to_jstooltip_text(cols_di, config, sec, "result_format_qc", "tooltip_format"), \
)
plots_option.append(chart_id)
# ID list
id_list = []
for row in df.data:
iid = row[df.name_to_index(cols_di["id"])]
if iid != "": id_list.append(iid)
id_list = list(set(id_list))
id_list.sort()
# header
headers = tools.dict_keys(cols_di)
f = open(output_file, "w")
f.write(js_header)
f.write(js_dataset.format(IDs = convert.list_to_text(id_list), \
header = convert.list_to_text(headers), \
plots = plots_text))
f.write(js_data1)
# values
for row in df.data:
iid = row[df.name_to_index(cols_di["id"])]
if iid == "": continue
values = ""
for item in headers:
if len(values) > 0:
values += ","
val = row[df.name_to_index(cols_di[item])]
if type(val) == type(""):
values += "'" + val + "'"
elif type(val) == type(0.0):
values += str('%.2f' % val)
else:
values += str(val)
f.write("[" + values + "],")
f.write(js_data2)
f_template = open(
os.path.dirname(os.path.abspath(__file__)) + "/templates/data_qc.js")
js_function = f_template.read()
f_template.close()
f.write(js_function)
f.write(js_footer)
f.close()
return {"plots": plots_option}
def convert_tojs(input_file, output_file, positions, config):
import paplot.subcode.data_frame as data_frame
import paplot.subcode.merge as merge
import paplot.subcode.tools as tools
import paplot.convert as convert
import paplot.color as color
cols_di = merge.position_to_dict(positions)
# data read
try:
df = data_frame.load_file(input_file, header = 1, \
sept = tools.config_getstr(config, "merge_format_qc", "sept"), \
comment = tools.config_getstr(config, "result_format_qc", "comment") \
)
except Exception as e:
print ("failure open data %s, %s" % (input_file, e.message))
return None
if len(df.data) == 0:
print ("no data %s" % input_file)
return None
# chart list
plots_text = ""
plots_option = []
config_sections = config.sections()
config_sections.sort()
if "qc_chart_brush" in config_sections:
config_sections.remove("qc_chart_brush")
config_sections.insert(0, "qc_chart_brush")
for sec in config.sections():
if not sec.startswith("qc_chart_"):
continue
chart_id = sec.replace("qc_chart_", "chart_")
stack_id = []
label = []
colors_di = {}
counter = 0
for name_set in tools.config_getstr(config, sec, "name_set").split(","):
name_set_split = convert.text_to_list(name_set, ":")
if len(name_set_split) == 0:
continue
stack_id.append("stack" + str(counter))
label.append(name_set_split[0])
if len(name_set_split) > 1:
colors_di[name_set_split[0]] = color.name_to_value(name_set_split[1])
counter += 1
# fill in undefined items
colors_di = color.create_color_dict(label, colors_di, color.metro_colors)
# dict to value
colors_li = []
for key in label:
colors_li.append(colors_di[key])
plots_text += plot_template.format(
chart_id = chart_id, \
title = tools.config_getstr(config, sec, "title"), \
title_y = tools.config_getstr(config, sec, "title_y"), \
stack = convert.pyformat_to_jstooltip_text(cols_di, config, sec, "result_format_qc", "stack"), \
stack_id = convert.list_to_text(stack_id), \
label = convert.list_to_text(label), \
color = convert.list_to_text(colors_li), \
tooltip = convert.pyformat_to_jstooltip_text(cols_di, config, sec, "result_format_qc", "tooltip_format"), \
)
plots_option.append(chart_id)
# ID list
Ids = []
for row in df.data:
iid = row[df.name_to_index(cols_di["id"])]
if iid != "": Ids.append(iid)
Ids = list(set(Ids))
Ids.sort()
# header
headers = cols_di.keys()
headers.sort()
f = open(output_file, "w")
f.write(js_header)
f.write(js_dataset.format(IDs = convert.list_to_text(Ids), \
header = convert.list_to_text(headers), \
plots = plots_text))
f.write(js_data1)
# values
for row in df.data:
iid = row[df.name_to_index(cols_di["id"])]
if iid == "": continue
values = ""
for item in headers:
if len(values) > 0:
values += ","
val = row[df.name_to_index(cols_di[item])]
if type(val) == type(""):
values += "'" + val + "'"
elif type(val) == type(0.0):
values += str('%.2f' % val)
else:
values += str(val)
f.write("[" + values + "],")
f.write(js_data2)
f.write(js_function)
f.close()
return {"plots": plots_option}
def load_subdata(ids, sec, config):
import os
import paplot.subcode.tools as tools
import paplot.convert as convert
import paplot.color as color
input_file = tools.config_getpath(config, sec, "path", default = "../../example/sample_summary.csv")
if os.path.exists(input_file) == False:
print ("[ERROR] file is not exist. %s" % input_file)
return None
sept = tools.config_getstr(config, sec, "sept")
mode = tools.config_getstr(config, sec, "mode")
comment = tools.config_getstr(config, sec, "comment")
title = tools.config_getstr(config, sec, "title")
label = []
item = []
colors_n_di = {}
colors_h_di = {}
for name_set in tools.config_getstr(config, sec, "name_set").split(","):
name_set_split = convert.text_to_list(name_set, ":")
for i in range(len(name_set_split)):
text = name_set_split[i]
if i == 0:
item.append(text)
if len(name_set_split) == 1:
label.append(text)
elif i == 1:
label.append(text)
elif i == 2:
colors_n_di[name_set_split[0]] = color.name_to_value(text)
elif i == 3:
colors_h_di[name_set_split[0]] = color.name_to_value(text)
# fill in undefined items
colors_n_di = color.create_color_dict(item, colors_n_di, color.osaka_subway_colors)
colors_h_di2 = {}
for key in colors_n_di:
if colors_h_di.has_key(key): continue
colors_h_di2[key] = color.Saturation_down(colors_n_di[key])
# dict to value
colors_n = []
for key in item:
colors_n.append(colors_n_di[key])
if mode == "range":
item.remove(item[0])
header = []
if tools.config_getboolean(config, sec, "header") == True:
pos_value = -1
pos_ID = -1
else:
pos_value = tools.config_getint(config, sec, "col_value")
pos_ID = tools.config_getint(config, sec, "col_ID")
header = ["",""]
# copy Ids for find check
unlookup = []
for iid in ids:
unlookup.append(iid)
# read
data_text = ""
values = []
for line in open(input_file):
line = line.strip()
if len(line.replace(sept, "")) == 0:
continue
if comment != "" and line.find(comment) == 0:
continue
if len(header) == 0:
header = convert.text_to_list(line,sept)
try:
colname = tools.config_getstr(config, sec, "col_value")
pos_value = header.index(colname)
colname = tools.config_getstr(config, sec, "col_ID")
pos_ID = header.index(colname)
except Exception as e:
print(e.message)
return None
continue
cols = convert.text_to_list(line,sept)
if (cols[pos_ID] in ids) == False: continue
else: unlookup.remove(cols[pos_ID])
id_pos = ids.index(cols[pos_ID])
if mode == "fix":
if cols[pos_value] in item:
data_text += subdata_data_template.format(id = id_pos, item = item.index(cols[pos_value]))
else:
print("[" + sec + "] name_set: data is undefined." + cols[pos_value] + "\n")
continue
elif mode == "range":
try:
values.append(float(cols[pos_value]))
except Exception as e:
print(colname + ": data type is invalid.\n" + e.message)
continue
data_text += subdata_data_template.format(id = id_pos, item = cols[pos_value])
elif mode == "gradient":
try:
values.append(float(cols[pos_value]))
except Exception as e:
print(colname + ": data type is invalid.\n" + e.message)
continue
data_text += subdata_data_template.format(id = id_pos, item = cols[pos_value])
if len(unlookup) > 0:
print("[WARNING] can't find IDs subplot data.")
print(unlookup)
if mode == "gradient" and len(values) > 0:
item[0] = min(values)
item[1] = max(values)
return [data_text, item, colors_n, label, title]
def group_list(colmun, mode, name, config):
"""
Create and return group names and their color values
Parameters
----------
colmun: list: colmun data for group title
mode : str : ca or mutation
name : str : "group"
config: configparser.RawConfigParser
Return
------
A nested list with elements funcs and colors
funcs : list: group names
colors: list: color values
"""
import paplot.color as color
# option_input: section name
option_input = ""
if mode == "mutation":
option_input = "result_format_mutation"
elif mode == "ca":
option_input = "result_format_ca"
else:
return []
# Get values from a configuration file
sept = tools.config_getstr(config, option_input,
"sept_%s" % name) # key: sept_group
limited_list = text_to_list(
tools.config_getstr(config, mode, "limited_%s" % name),
",") # key: limited_group
nouse_list = text_to_list(
tools.config_getstr(config, mode, "nouse_%s" % name),
",") # key: nouse_group
# Create funcs that is a list with group names as elements
funcs = []
for row in colmun:
# Split row if necessary
splt = []
if sept == "":
splt.append(row)
else:
splt = row.split(sept)
# Limit the elements to be added to funcs
for func in splt:
func = func.strip()
# Ignore empty string
if func == "":
continue
# Ignore if func is not in non-empty limited_list
if len(limited_list) > 0 and fnmatch_list(func,
limited_list) is False:
continue
# Ignore if func is in nouse_list
if fnmatch_list(func, nouse_list):
continue
funcs.append(func)
# Sort after eliminating duplicated elements of funcs
funcs = list(set(funcs))
funcs.sort()
# Create color_di that is a dictionary with group names as keys and color values as values
color_di = {}
for f in tools.config_getstr(config, mode, "%s_color" %
name).split(","): # key: group_color
# Ignore empty string
if len(f) == 0:
continue
# f assumes something like "A:#66C2A5"
cols = text_to_list(f, ":")
if len(cols) >= 2:
color_di[cols[0]] = color.name_to_value(cols[1])
# Determine color values for groups
color_di = color.create_color_dict(funcs, color_di, color.metro_colors)
# Create color list for groups
colors = []
for key in funcs:
colors.append(color_di[key])
return [funcs, colors]
