def main():
matrixfile = sys.argv[1]
g2sfile = sys.argv[2]
outdir = sys.argv[3]
# read in matrix:
r2c2count = read_matrix(matrixfile)
# group info:
groups, g2s, matched = read_group_info(g2sfile)
pair2count = get_pair2count(r2c2count)
# get distribution (draw dist and get outliers)
lowpoint, uppoint = get_dist(pair2count, g2s, outdir)
# re draw group comparison boxplot with lims:
group_cmp(pair2count, g2s, lowpoint, uppoint, outdir)
# draw heatmap:
s2g = lcommon.get_val2key_1to1(g2s)
s2color = dcommon.get_name2color_wtgroup(s2g.keys(), s2g, g2s)
heatmap_file = os.path.join(outdir, "heatmap.pdf")
names = []
for g, gnames in g2s.iteritems():
for n in gnames:
if n in r2c2count:
names.append(n)
draw_heatmap(r2c2count, s2color, lowpoint, uppoint, heatmap_file, names)
def samples_group_info(names, g2names, groups, matched):
n2group = {}
n2color = {}
n2marker = {}
if g2names:
n2group = libcommon.get_val2key_1to1(g2names)
n2color = drawcommon.get_name2color_wtgroup(names, n2group, g2names, groups, matched)
n2marker = drawcommon.get_name2marker_wtgroup(names, g2names)
return n2group, n2color, n2marker
def run(self):
opts = self.opts
sample2group = libcommon.get_val2key_1to1(opts.group2samples)
global_dir = self.getGlobalTempDir()
tc_dir = os.path.join(global_dir, "trackclone_%s" %
os.path.basename(self.outdir.rstrip('/')))
system("mkdir -p %s" % tc_dir)
for clone in self.clones:
outfile = os.path.join(tc_dir, "%s.pickle" % clone)
self.addChildTarget(TrackClone(clone, self.indir, outfile, opts,
sample2group))
self.setFollowOnTarget(TrackClonesAgg(tc_dir, self.outdir, opts))