comparison scatterplot.py @ 1:b4102b163488 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty

0:11627baf830e

# Greg Von Kuster

import sys

from numpy import array
from rpy import r


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

        if valid:
            matrix.append( row )

    if skipped_lines < i:
        try:
            r.pdf( out_fname, 8, 8 )
            r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
            r.dev_off()
        except Exception, 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 )

    r.quit( save="no" )

if __name__ == "__main__":
    main()

1:b4102b163488

# Greg Von Kuster

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()

        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, 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()