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VUmcCGP / wisecondor

WISECONDOR (WIthin-SamplE COpy Number aberration DetectOR): Detect fetal trisomies and smaller CNV's in a maternal plasma sample using whole-genome data.
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Cytobands do not scale in plots #31

Closed rstraver closed 7 years ago

rstraver commented 7 years ago

Looks like I forgot to use the actual bin size of the output file instead of the default 250k bins. If you use 1mb bins rather than 250kb, the cytobands don't make sense at all (same goes for any other bin size) this should fix it:

Add this argument in the function call starting at line 284:

      binsize=resultFile['binsize'],

Final function call should look like this:

def toolPlot(args):
    resultFile = np.load(args.infile)
    name = args.infile.split('/')[-1].split('.')[0]

    plotLines(resultFile['results_z'], resultFile['results_calls'], resultFile['threshold_z'],
        sampleName=name,
        minEffect=args.mineffect,
        binsize=resultFile['binsize'],
        cytoFile=args.cytofile,
        chromosomes=args.chromosomes,
        columns=args.columns,
        size=args.size).savefig(args.outfile+'_z.'+args.filetype)