comparison scatterplot.py @ 2:53eb2c412783 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit de7140295cce07e1bc1697e51dab4271c8d7a8a6

1:4afd68392187

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

import sys
from rpy import *

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

def main():

    in_fname = sys.argv[1]
    out_fname = sys.argv[2]

    invalid_column = 0
    i = 0
    for i, line in enumerate( file( 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:
                    valid = False

                    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:
            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:

2:53eb2c412783

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

import sys

from numpy import array
from rpy import r


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


def main():

    in_fname = sys.argv[1]
    out_fname = sys.argv[2]

    invalid_column = 0
    i = 0
    for i, line in enumerate( file( 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:
                    valid = False

                    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:
            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: