def plot_heatmap(tsv, options):
""" make a heatmap """
out_dir = os.path.join(options.comp_dir, "heatmaps")
robust_makedirs(out_dir)
mat, col_names, row_names, row_label = read_tsv(tsv)
names = name_map()
for i in range(len(col_names)):
if col_names[i] in names:
col_names[i] = names[col_names[i]]
for i in range(len(row_names)):
if row_names[i] in names:
row_names[i] = names[row_names[i]]
if "_rename" in tsv:
return
fix_tsv = tsv.replace(".tsv", "_rename.tsv")
write_tsv(fix_tsv, mat, col_names, row_names, row_label)
out_hm = os.path.join(out_dir, os.path.basename(tsv).replace(".tsv", ".pdf"))
ph_opts = "--skip {}".format(options.skip) if options.skip is not None else ""
cmd = "scripts/plotHeatmap.py {} {} {}".format(fix_tsv, out_hm, ph_opts)
print cmd
os.system(cmd)
cmd = "scripts/plotHeatmap.py {} {} {} --log_scale".format(fix_tsv, out_hm.replace(".pdf", "_log.pdf"), ph_opts)
print cmd
os.system(cmd)
def plot_heatmap(tsv, options):
""" make a heatmap """
out_dir = os.path.join(options.comp_dir, "heatmaps")
robust_makedirs(out_dir)
mat, col_names, row_names, row_label = read_tsv(tsv)
names = name_map()
for i in range(len(col_names)):
if col_names[i] in names:
col_names[i] = names[col_names[i]]
for i in range(len(row_names)):
if row_names[i] in names:
row_names[i] = names[row_names[i]]
if "_rename" in tsv:
return
fix_tsv = tsv.replace(".tsv", "_rename.tsv")
write_tsv(fix_tsv, mat, col_names, row_names, row_label)
out_hm = os.path.join(out_dir, os.path.basename(tsv).replace(".tsv", ".pdf"))
ph_opts = "--skip {}".format(options.skip) if options.skip is not None else ""
cmd = "scripts/plotHeatmap.py {} {} {}".format(fix_tsv, out_hm, ph_opts)
print cmd
os.system(cmd)
cmd = "scripts/plotHeatmap.py {} {} {} --log_scale".format(fix_tsv, out_hm.replace(".pdf", "_log.pdf"), ph_opts)
print cmd
os.system(cmd)
def main(args):
options = parse_args(args)
assert os.path.splitext(options.out_file)[1] == ".pdf"
options.skip = options.skip.split(",")
mat, col_names, row_names, row_label = read_tsv(options.dist_mat)
mat, col_names, row_names = remove_skips(mat, col_names, row_names, options.skip)
plotHeatMap(mat, row_names, col_names,
options.out_file,
leftTree=True,
topTree=True,
logNorm=options.log_scale,
vmax=options.vmax)
def main(args):
options = parse_args(args)
assert os.path.splitext(options.out_file)[1] == ".pdf"
options.skip = options.skip.split(",")
mat, col_names, row_names, row_label = read_tsv(options.dist_mat)
mat, col_names, row_names = remove_skips(mat, col_names, row_names,
options.skip)
plotHeatMap(mat,
row_names,
col_names,
options.out_file,
leftTree=True,
topTree=True,
logNorm=options.log_scale,
vmax=options.vmax)
