def run(self): #name2obj = libcommon.load_pickledir_to_dict(self.indir) self.load_indir() name2obj = self.name2obj attrs = ['clones', 'reads'] plotfmt = self.opts.plotformat if not self.avr and len(name2obj) >= 20: self.avr = True for attr in attrs: plotfile = os.path.join(self.outdir, "%s" % attr) #if len(name2obj) >= 20: if self.avr: ldplot.draw_lendist_avr(name2obj, attr, plotfile, plotfmt, self.opts.dpi, bar=True) #self.opts.dpi) else: ldplot.draw_lendist(name2obj, attr, plotfile, plotfmt, self.opts.dpi) # ttests g2n = self.opts.group2samples if g2n: ttestfile = os.path.join(self.outdir, "ttests_%s.txt" % attr) lendist_ttests(attr, ttestfile, g2n, name2obj, self.opts.matched, self.opts.pval) # median len distribution meddist_file = os.path.join(self.outdir, "median_lendist_%s.txt" % attr) lendist_median(name2obj, attr, meddist_file)
def draw_plots(name2obj, outdir): vfile = os.path.join(outdir, "v") vgenes = union_lists([obj.type2gene2clones['v'].keys() for obj in name2obj.values()]) draw_gene_usage(name2obj, "clones", "v", vfile, vgenes) jfile = os.path.join(outdir, "j") jgenes = union_lists([obj.type2gene2clones['j'].keys() for obj in name2obj.values()]) draw_gene_usage(name2obj, "clones", "j", jfile, jgenes) lfile = os.path.join(outdir, "lendist") draw_lendist(name2obj, "clones", lfile)