Mercurial > repos > fubar > lifelines_km_cph_tool
view lifelines_tool/plotlykm.py @ 0:dd49a7040643 draft
Initial commit
author | fubar |
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date | Wed, 09 Aug 2023 11:12:16 +0000 |
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children | 232b874046a7 |
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# script for a lifelines ToolFactory KM/CPH tool for Galaxy # km models for https://github.com/galaxyproject/tools-iuc/issues/5393 # test as # python plotlykm.py --input_tab rossi.tab --htmlout "testfoo" --time "week" --status "arrest" --title "test" --image_dir images --cphcol="prio,age,race,paro,mar,fin" import argparse import os import sys import lifelines from matplotlib import pyplot as plt import pandas as pd # Ross Lazarus July 2023 kmf = lifelines.KaplanMeierFitter() cph = lifelines.CoxPHFitter() parser = argparse.ArgumentParser() a = parser.add_argument a('--input_tab', default='', required=True) a('--header', default='') a('--htmlout', default="test_run.html") a('--group', default='') a('--time', default='', required=True) a('--status',default='', required=True) a('--cphcols',default='') a('--title', default='Default plot title') a('--image_type', default='png') a('--image_dir', default='images') a('--readme', default='run_log.txt') args = parser.parse_args() sys.stdout = open(args.readme, 'w') df = pd.read_csv(args.input_tab, sep='\t') NCOLS = df.columns.size NROWS = len(df.index) defaultcols = ['col%d' % (x+1) for x in range(NCOLS)] testcols = df.columns if len(args.header.strip()) > 0: newcols = args.header.split(',') if len(newcols) == NCOLS: if (args.time in newcols) and (args.status in newcols): df.columns = newcols else: sys.stderr.write('## CRITICAL USAGE ERROR (not a bug!): time %s and/or status %s not found in supplied header parameter %s' % (args.time, args.status, args.header)) sys.exit(4) else: sys.stderr.write('## CRITICAL USAGE ERROR (not a bug!): Supplied header %s has %d comma delimited header names - does not match the input tabular file %d columns' % (args.header, len(newcols), NCOLS)) sys.exit(5) else: # no header supplied - check for a real one that matches the x and y axis column names colsok = (args.time in testcols) and (args.status in testcols) # if they match, probably ok...should use more code and logic.. if colsok: df.columns = testcols # use actual header else: colsok = (args.time in defaultcols) and (args.status in defaultcols) if colsok: sys.stderr.write('replacing first row of data derived header %s with %s' % (testcols, defaultcols)) df.columns = defaultcols else: sys.stderr.write('## CRITICAL USAGE ERROR (not a bug!): time %s and status %s do not match anything in the file header, supplied header or automatic default column names %s' % (args.time, args.status, defaultcols)) print('## Lifelines tool starting.\nUsing data header =', df.columns, 'time column =', args.time, 'status column =', args.status) os.makedirs(args.image_dir, exist_ok=True) fig, ax = plt.subplots() if args.group > '': names = [] times = [] events = [] rmst = [] for name, grouped_df in df.groupby(args.group): T = grouped_df[args.time] E = grouped_df[args.status] gfit = kmf.fit(T, E, label=name) kmf.plot_survival_function(ax=ax) rst = lifelines.utils.restricted_mean_survival_time(gfit) rmst.append(rst) names.append(str(name)) times.append(T) events.append(E) ngroup = len(names) if ngroup == 2: # run logrank test if 2 groups results = lifelines.statistics.logrank_test(times[0], times[1], events[0], events[1], alpha=.99) print(' vs '.join(names), results) results.print_summary() elif ngroup > 1: fig, ax = plt.subplots(nrows=ngroup, ncols=1, sharex=True) for i, rst in rmst: lifelines.plotting.rmst_plot(rst, ax=ax) fig.savefig(os.path.join(args.image_dir,'RMST_%s.png' % args.title)) else: kmf.fit(df[args.time], df[args.status]) kmf.plot_survival_function(ax=ax) fig.savefig(os.path.join(args.image_dir,'KM_%s.png' % args.title)) if len(args.cphcols) > 0: fig, ax = plt.subplots() cphcols = args.cphcols.strip().split(',') cphcols = [x.strip() for x in cphcols] notfound = sum([(x not in df.columns) for x in cphcols]) if notfound > 0: sys.stderr.write('## CRITICAL USAGE ERROR (not a bug!): One or more requested Cox PH columns %s not found in supplied column header %s' % (args.cphcols, df.columns)) sys.exit(6) print('### Lifelines test of Proportional Hazards results with %s as covariates on %s' % (', '.join(cphcols), args.title)) cphcols += [args.time, args.status] cphdf = df[cphcols] cph.fit(cphdf, duration_col=args.time, event_col=args.status) cph.print_summary() cphaxes = cph.check_assumptions(cphdf, p_value_threshold=0.01, show_plots=True) for i, ax in enumerate(cphaxes): figr = ax[0].get_figure() titl = figr._suptitle.get_text().replace(' ','_').replace("'","") oname = os.path.join(args.image_dir,'CPH%s.%s' % (titl, args.image_type)) figr.savefig(oname)