Added tool version directories for plotting tools directory.

tools/plotting/scatterplot.py

@@ -1,79 +0,0 @@
-#!/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]
-    try:
-        columns = int( sys.argv[3] ) - 1, int( sys.argv[4] ) - 1
-    except:
-        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
-
-    for i, line in enumerate( file ( sys.argv[1] ) ):
-        valid = True
-        line = line.rstrip('\r\n')
-        if line and not line.startswith( '#' ): 
-            # Extract values and convert to floats
-            row = []
-            for column in columns:
-                if not valid:
-                    break
-                fields = line.split( "\t" )
-                if len( fields ) <= column:
-                    stop_err( "Column %d on line %d missing, line: %s" % ( column+1, i, line ) )
-                val = fields[column]
-                if val.lower() == "na": 
-                    row.append( float( "nan" ) )
-                else:
-                    try:
-                        row.append( float( fields[column] ) )
-                    except:
-                        valid = False
-                        skipped_lines += 1
-                        if not first_invalid_line:
-                            first_invalid_line = i+1
-                            invalid_value = fields[column]
-                            invalid_column = column+1
-        else:
-            valid = False
-            skipped_lines += 1
-            if not first_invalid_line:
-                first_invalid_line = i+1
-
-        if valid:
-            matrix.append( row )
-        
-    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()
-
-    msg = "--Scatter plot on "
-    for i,col in enumerate(columns):
-        col += 1
-        msg += "c%d, " %col
-    if skipped_lines > 0:
-        msg += " skipped %d lines starting with line #%d.  Value '%s' in column %d is not numeric." % ( skipped_lines, first_invalid_line, invalid_value, invalid_column )
-
-    print msg
-
-    r.quit( save="no" )
-
-if __name__ == "__main__":
-    main()