Mercurial > repos > peterjc > venn_list
diff tools/venn_list/venn_list.py @ 11:679b6323db03 draft
v0.1.0 now using matplotlib_venn instead of limma R package via rpy. Contribution from Frederic Sapet.
author | peterjc |
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date | Wed, 29 May 2019 04:45:19 -0400 |
parents | 20d347feb882 |
children |
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--- a/tools/venn_list/venn_list.py Thu May 11 07:02:57 2017 -0400 +++ b/tools/venn_list/venn_list.py Wed May 29 04:45:19 2019 -0400 @@ -1,5 +1,9 @@ #!/usr/bin/env python -"""Plot up to 3-way Venn Diagram using R limma vennDiagram (via rpy) + +""" +Plot up to 3-way Venn Diagram. + +It uses the Python libraries matplotlib and matplotlib_venn. This script is copyright 2010-2017 by Peter Cock, The James Hutton Institute (formerly SCRI), UK. All rights reserved. @@ -10,26 +14,25 @@ from __future__ import print_function import sys +from shutil import move if "-v" in sys.argv or "--version" in sys.argv: - print("v0.0.11") + print("v0.1.0") sys.exit(0) try: - import rpy + import matplotlib except ImportError: - sys.exit("Requires the Python library rpy (to call R)") -except RuntimeError, e: - sys.exit("The Python library rpy is not availble for the current R version\n\n%s" % e) + sys.exit("Requires the Python library matplotlib") -try: - rpy.r.library("limma") -except Exception: - sys.exit("Requires the R library limma (for vennDiagram function)") - +matplotlib.use("Agg") +from matplotlib import pyplot as plt if len(sys.argv) - 1 not in [7, 10, 13]: - sys.exit("Expected 7, 10 or 13 arguments (for 1, 2 or 3 sets), not %i" % (len(sys.argv) - 1)) + sys.exit( + "Expected 7, 10 or 13 arguments (for 1, 2 or 3 sets), not %i" + % (len(sys.argv) - 1) + ) all_file, all_type, all_label = sys.argv[1:4] set_data = [] @@ -45,6 +48,7 @@ def load_ids(filename, filetype): + """Load ids from files.""" if filetype == "tabular": for line in open(filename): line = line.rstrip("\n") @@ -57,6 +61,7 @@ elif filetype.startswith("fastq"): # Use the Galaxy library not Biopython to cope with CS from galaxy_utils.sequence.fastq import fastqReader + handle = open(filename, "rU") for record in fastqReader(handle): # The [1:] is because the fastaReader leaves the @ on the identifer. @@ -68,18 +73,21 @@ except ImportError: sys.exit("Require Biopython 1.54 or later (to read SFF files)") # This will read the SFF index block if present (very fast) - for name in index(filename, "sff"): - yield name + for this_name in index(filename, "sff"): + yield this_name else: sys.exit("Unexpected file type %s" % filetype) def load_ids_whitelist(filename, filetype, whitelist): - for name in load_ids(filename, filetype): - if name in whitelist: - yield name + """Check if ids are in whitelist.""" + for single_name in load_ids(filename, filetype): + if single_name in whitelist: + yield single_name else: - sys.exit("Unexpected ID %s in %s file %s" % (name, filetype, filename)) + sys.exit( + "Unexpected ID %s in %s file %s" % (single_name, filetype, filename) + ) if all_file in ["", "-", '""', '"-"']: @@ -98,42 +106,54 @@ for s, (f, t, c) in zip(sets, set_data): print("%i in %s" % (len(s), c)) -# Now call R library to draw simple Venn diagram +names = [one_name for one_file, one_type, one_name in set_data] +lengths = [len(one_set) for one_set in sets] + +if len(sets) == 3: + try: + from matplotlib_venn import venn3_unweighted + except ImportError: + sys.exit("Requires the Python library matplotlib_venn") + venn3_unweighted( + sets, + [ + "{} (Total {})".format(name, length) + for (name, length) in zip(names, lengths) + ], + ) + +if len(sets) == 2: + try: + from matplotlib_venn import venn2_unweighted + except ImportError: + sys.exit("Requires the Python library matplotlib_venn") + venn2_unweighted( + sets, + [ + "{} (Total {})".format(name, length) + for (name, length) in zip(names, lengths) + ], + ) + +# not sure what I am doing here, +# matplotlib_venn does not want to create a single Venn circle +# stick to the old behavior (rpy and Limma) as much as possible +if len(sets) == 1: + try: + from matplotlib_venn import venn2 + except ImportError: + sys.exit("Requires the Python library matplotlib_venn") + venn2((sets[0], set()), [set_data[0][2], ""]) + +plt.title(all_label) +plt.savefig(pdf_file + ".pdf") + +# Format "dat" is not supported. try: - # Create dummy Venn diagram counts object for three groups - cols = 'c("%s")' % '","'.join("Set%i" % (i + 1) for i in range(n)) - rpy.r('groups <- cbind(%s)' % ','.join(['1'] * n)) - rpy.r('colnames(groups) <- %s' % cols) - rpy.r('vc <- vennCounts(groups)') - # Populate the 2^n classes with real counts - # Don't make any assumptions about the class order - # print(rpy.r('vc')) - for index, row in enumerate(rpy.r('vc[,%s]' % cols)): - if isinstance(row, int) or isinstance(row, float): - # Hack for rpy being too clever for single element row - row = [row] - names = all_ids - for wanted, s in zip(row, sets): - if wanted: - names = names.intersection(s) - else: - names = names.difference(s) - rpy.r('vc[%i,"Counts"] <- %i' % (index + 1, len(names))) - # print(rpy.r('vc')) - if n == 1: - # Single circle, don't need to add (Total XXX) line - names = [c for (t, f, c) in set_data] - else: - names = ["%s\n(Total %i)" % (c, len(s)) for s, (f, t, c) in zip(sets, set_data)] - rpy.r.assign("names", names) - rpy.r.assign("colors", ["red", "green", "blue"][:n]) - rpy.r.pdf(pdf_file, 8, 8) - rpy.r("""vennDiagram(vc, include="both", names=names, - main="%s", sub="(Total %i)", - circle.col=colors) - """ % (all_label, len(all_ids))) - rpy.r.dev_off() -except Exception, exc: - sys.exit("%s" % str(exc)) -rpy.r.quit(save="no") + move(pdf_file + ".pdf", pdf_file) +except (OSError, IOError) as error: + sys.exit("Fail to rename file {}".format(str(error))) + +plt.close() + print("Done")