--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/plotting/histogram.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+#Greg Von Kuster
+
+import sys
+from rpy import *
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+
+def main():
+
+    # Handle input params
+    in_fname = sys.argv[1]
+    out_fname = sys.argv[2] 
+    try:
+        column = int( sys.argv[3] ) - 1
+    except:
+        stop_err( "Column not specified, your query does not contain a column of numerical data." )
+    title = sys.argv[4]
+    xlab = sys.argv[5]
+    breaks = int( sys.argv[6] )
+    if breaks == 0:
+        breaks = "Sturges"
+    if sys.argv[7] == "true":
+        density = True
+    else: density = False
+    if len( sys.argv ) >= 9 and sys.argv[8] == "true":
+        frequency = True
+    else: frequency = False
+
+    matrix = []
+    skipped_lines = 0
+    first_invalid_line = 0
+    invalid_value = ''
+    i = 0
+    for i, line in enumerate( file( in_fname ) ):
+        valid = True
+        line = line.rstrip('\r\n')
+        # Skip comments
+        if line and not line.startswith( '#' ): 
+            # Extract values and convert to floats
+            row = []
+            try:
+                fields = line.split( "\t" )
+                val = fields[column]
+                if val.lower() == "na":
+                    row.append( float( "nan" ) )
+            except:
+                valid = False
+                skipped_lines += 1
+                if not first_invalid_line:
+                    first_invalid_line = i+1
+            else:
+                try:
+                    row.append( float( val ) )
+                except ValueError:
+                    valid = False
+                    skipped_lines += 1
+                    if not first_invalid_line:
+                        first_invalid_line = i+1
+                        invalid_value = fields[column]
+        else:
+            valid = False
+            skipped_lines += 1
+            if not first_invalid_line:
+                first_invalid_line = i+1
+
+        if valid:
+            matrix += row
+
+    if skipped_lines < i:
+        try:
+            a = r.array( matrix )
+            r.pdf( out_fname, 8, 8 )
+            histogram = r.hist( a, probability=not frequency, main=title, xlab=xlab, breaks=breaks )
+            if density:
+                density = r.density( a )
+                if frequency:
+                    scale_factor = len( matrix ) * ( histogram['mids'][1] - histogram['mids'][0] ) #uniform bandwidth taken from first 2 midpoints
+                    density[ 'y' ] = map( lambda x: x * scale_factor, density[ 'y' ] )
+                r.lines( density )
+            r.dev_off()
+        except Exception, exc:
+            stop_err( "%s" %str( exc ) )
+    else:
+        if i == 0:
+            stop_err("Input dataset is empty.")
+        else:
+            stop_err( "All values in column %s are non-numeric." %sys.argv[3] )
+
+    print "Histogram of column %s. " %sys.argv[3]
+    if skipped_lines > 0:
+        print "Skipped %d invalid lines starting with line #%d, '%s'." % ( skipped_lines, first_invalid_line, invalid_value )
+
+    r.quit( save="no" )
+    
+if __name__ == "__main__":
+    main()