Merge branch 'features/heatmap_and_clustermap_script' into 'master'

Add script that generates heatmap and clustermap

See merge request zavolan_group/pipelines/rnaseqpipeline!3

scripts/heatmap_and_clustermap.py

+#!/usr/bin/env python
+
+# _____________________________________________________________________________
+# -----------------------------------------------------------------------------
+# import needed (external) modules
+# -----------------------------------------------------------------------------
+
+import sys
+import os
+import pandas as pd
+import numpy as np
+import seaborn as sns
+import matplotlib.pyplot as plt
+from argparse import ArgumentParser, RawTextHelpFormatter
+
+# _____________________________________________________________________________
+# -----------------------------------------------------------------------------
+# Main function
+# -----------------------------------------------------------------------------
+
+
+def main():
+    """ Main function """
+
+    __doc__ = "Create heatmap and clustermap based on a table (rows are genes/transcripts, columns are samples)."
+
+    parser = ArgumentParser(
+        description=__doc__,
+        formatter_class=RawTextHelpFormatter
+    )
+
+    parser.add_argument(
+        "--tpm",
+        dest="tpm",
+        help="TPM table (tsv)",
+        required=True,
+        metavar="FILE"
+    )
+
+    parser.add_argument(
+        "--out",
+        dest="out",
+        help="Output directory",
+        required=True,
+        metavar="FILE"
+    )
+
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="store_true",
+        dest="verbose",
+        default=False,
+        required=False,
+        help="Verbose"
+    )
+
+    # _________________________________________________________________________
+    # -------------------------------------------------------------------------
+    # get the arguments
+    # -------------------------------------------------------------------------
+    try:
+        options = parser.parse_args()
+    except(Exception):
+        parser.print_help()
+
+    if len(sys.argv) == 1:
+        parser.print_help()
+        sys.exit(1)
+
+    if options.verbose:
+        sys.stdout.write(f"Creating output directory: {options.out} {os.linesep}")
+
+    if not os.path.exists(options.out):
+        os.makedirs(options.out)
+
+    if options.verbose:
+        sys.stdout.write(f"Reading: {options.tpm} {os.linesep}")
+    df = pd.read_csv(options.tpm, header=0, sep="\t")
+    df.set_index(["Name"], inplace=True)
+    df = df + 1/32
+    df = np.log2(df)
+
+    if options.verbose:
+        sys.stdout.write(f"Generating heatmap {os.linesep}")
+
+    plt.rcParams["figure.figsize"] = (20,20)
+    g = sns.heatmap(df.corr(method="pearson"))
+    plt.savefig(os.path.join(options.out, "heatmap.pdf"))
+
+    if options.verbose:
+        sys.stdout.write(f"Generating clustermap {os.linesep}")
+
+    plt.rcParams["figure.figsize"] = (20,20)
+    g = sns.clustermap(df.corr(method="pearson"))
+    plt.savefig(os.path.join(options.out, "clustermap.pdf"))
+
+    if options.verbose:
+        sys.stdout.write(f"Done {os.linesep}")
+
+# _____________________________________________________________________________
+# -----------------------------------------------------------------------------
+# Call the Main function and catch Keyboard interrups
+# -----------------------------------------------------------------------------
+
+
+if __name__ == '__main__':
+    try:
+        main()
+    except KeyboardInterrupt:
+        sys.stderr.write("User interrupt!" + os.linesep)
+        sys.exit(0)