def markerPlot(self, options):
"""Marker gene position plot command"""
self.logger.info(
'[CheckM - marker_plot] Creating marker gene position plot.')
checkDirExists(options.bin_dir)
makeSurePathExists(options.output_dir)
# generate plot for each bin
binFiles = self.binFiles(options.bin_dir, options.extension)
resultsParser = ResultsParser(None)
markerGeneStats = resultsParser.parseMarkerGeneStats(
options.results_dir)
binStats = resultsParser.parseBinStatsExt(options.results_dir)
plot = MarkerGenePosPlot(options)
filesProcessed = 1
for f in binFiles:
binId = binIdFromFilename(f)
self.logger.info(
'Plotting marker gene position plot for %s (%d of %d)' %
(binId, filesProcessed, len(binFiles)))
filesProcessed += 1
if binId not in markerGeneStats or binId not in binStats:
continue # bin has no marker genes
bPlotted = plot.plot(f, markerGeneStats[binId], binStats[binId])
if bPlotted:
outputFile = os.path.join(
options.output_dir,
binId) + '.marker_pos_plot.' + options.image_type
plot.savePlot(outputFile, dpi=options.dpi)
self.logger.info('Plot written to: ' + outputFile)
else:
self.logger.info('No marker genes found in bin.')
self.timeKeeper.printTimeStamp()
