tools-devteam/tools/scatterplot/scatterplot.py at 3bae6a71438bcafed0e7ba36e695ee080c5bcfca · galaxyproject/tools-devteam · GitHub

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#!/usr/bin/env python
# Greg Von Kuster

# flake8: noqa

from __future__ import print_function

import sys

from numpy import array
import rpy2.rpy_classic as rpy
from rpy2.robjects.numpy2ri import numpy2ri


rpy.set_default_mode(rpy.NO_CONVERSION)
r = rpy.r


def stop_err(msg):
    sys.stderr.write(msg)
    sys.exit()


def main():

    in_fname = sys.argv[1]
    out_fname = sys.argv[2]
    try:
        columns = int(sys.argv[3]) - 1, int(sys.argv[4]) - 1
    except Exception:
        stop_err(
            "Columns not specified, your query does not contain a column of numerical data."
        )
    title = sys.argv[5]
    xlab = sys.argv[6]
    ylab = sys.argv[7]

    matrix = []
    skipped_lines = 0
    first_invalid_line = 0
    invalid_value = ""
    invalid_column = 0
    i = 0
    for i, line in enumerate(open(in_fname)):
        valid = True
        line = line.rstrip("\r\n")
        if line and not line.startswith("#"):
            row = []
            fields = line.split("\t")
            for column in columns:
                try:
                    val = fields[column]
                    if val.lower() == "na":
                        row.append(float("nan"))
                    else:
                        row.append(float(fields[column]))
                except Exception:
                    valid = False
                    skipped_lines += 1
                    if not first_invalid_line:
                        first_invalid_line = i + 1
                        try:
                            invalid_value = fields[column]
                        except Exception:
                            invalid_value = ""
                        invalid_column = column + 1
                    break
        else:
            valid = False
            skipped_lines += 1
            if not first_invalid_line:
                first_invalid_line = i + 1

        if valid:
            matrix.append(row)

    if skipped_lines < i:
        try:
            a = numpy2ri(array(matrix))
            r.pdf(out_fname, 8, 8)
            r.plot(a, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19)
            r.dev_off()
        except Exception as exc:
            stop_err("%s" % str(exc))
    else:
        stop_err(
            "All values in both columns %s and %s are non-numeric or empty."
            % (sys.argv[3], sys.argv[4])
        )

    print("Scatter plot on columns %s, %s. " % (sys.argv[3], sys.argv[4]))
    if skipped_lines > 0:
        print(
            "Skipped %d lines starting with line #%d, value '%s' in column %d is not numeric."
            % (skipped_lines, first_invalid_line, invalid_value, invalid_column)
        )


if __name__ == "__main__":
    main()