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1 #!/usr/bin/env python
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2 """
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3 Author: Timothy Tickle
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4 Description: Plots feaures
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5 """
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6
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7 __author__ = "Timothy Tickle"
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8 __copyright__ = "Copyright 2012"
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9 __credits__ = ["Timothy Tickle"]
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10 __license__ = ""
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11 __version__ = ""
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12 __maintainer__ = "Timothy Tickle"
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13 __email__ = "ttickle@sph.harvard.edu"
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14 __status__ = "Development"
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15
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16 import sys
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17 import argparse
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18 import csv
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19 import os
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20 from src.BoxPlot import BoxPlot
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21 from src.Histogram import Histogram
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22 from src.ScatterPlot import ScatterPlot
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23
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24 def funcPlotBoxPlot(lxVariable1,lxVariable2,fOneIsNumeric):
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25
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26 ly,lsLabels = [lxVariable1,lxVariable2] if fOneIsNumeric else [lxVariable2,lxVariable1]
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27
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28 # Group data
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29 dictGroups = {}
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30 for iIndex in xrange(len(ly)):
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31 lsList = dictGroups.get(lsLabels[iIndex],[])
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32 lsList.append(ly[iIndex])
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33 dictGroups.setdefault(lsLabels[iIndex],lsList)
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34 ly = [dictGroups[sKey] for sKey in dictGroups.keys()]
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35 lsLabels = dictGroups.keys()
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36
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37 BoxPlot.funcPlot(ly=ly, lsLabels=lsLabels, strOutputFigurePath=args.strOutputFile, strTitle=args.strTitle, strXTitle=args.strX, strYTitle=args.strY, strColor=args.strColor, fJitter=True, fInvert=args.fColor, fInvertY=args.fAxis)
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38
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39
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40 #Set up arguments reader
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41 argp = argparse.ArgumentParser( prog = "scriptBoxPlot.py\nExample: python scriptBoxPlot.py Input.pcl valuesID groupID",
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42 description = "Make a box plot from an abundance table.")
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43
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44 #Sepecify output if needed
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45 argp.add_argument("-o","--output", dest="strOutputFile", action="store", default=None, help="Output file name.")
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46
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47 # Text annotation
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48 argp.add_argument("-t","--title", dest="strTitle", action="store", default=None, help="Test for the title.")
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49 argp.add_argument("-x","--xaxis", dest="strX", action="store", default=None, help="Text for the x-axis.")
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50 argp.add_argument("-y","--yaxis", dest="strY", action="store", default=None, help="Text for the y-axis.")
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51
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52 # Color options
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53 argp.add_argument("-c","--color", dest="strColor", action="store", default="#83C8F9", help="Fill color as a Hex number (including the #).")
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54 argp.add_argument("-r","--invertcolor", dest="fColor", action="store_true", default=False, help="Flag to invert the background to black.")
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55
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56 # Axis adjustments
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57 argp.add_argument("-s","--invertyaxis", dest="fAxis", action="store_true", default=False, help="Flag to invert the y axis.")
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58
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59 # Required
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60 argp.add_argument("strFileAbund", help ="Input data file")
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61 argp.add_argument("strFeatures", nargs = "+", help="Features to plot (from one to two metadata).")
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62
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63 args = argp.parse_args( )
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64
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65 #Holds the data
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66 lxVariable1 = None
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67 lxVariable2 = None
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68 fOneIsNumeric = False
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69 fTwoIsNumeric = False
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70
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71 strFeatureOneID = args.strFeatures[0]
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72 strFeatureTwoID = None if len(args.strFeatures)<2 else args.strFeatures[1]
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73
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74 # If the output file is not specified, make it up
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75 if not args.strOutputFile:
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76 lsPieces = os.path.splitext(args.strFileAbund)
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77 args.strOutputFile = [lsPieces[0],strFeatureOneID]
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78 if strFeatureTwoID:
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79 args.strOutputFile = args.strOutputFile+[strFeatureTwoID]
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80 args.strOutputFile = "-".join(args.strOutputFile+["plotfeature.pdf"])
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81
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82 if not args.strTitle:
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83 args.strTitle = [strFeatureOneID]
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84 if strFeatureTwoID:
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85 args.strTitle = args.strTitle+[strFeatureTwoID]
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86 args.strTitle = " vs ".join(args.strTitle)
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87
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88 csvReader = csv.reader(open(args.strFileAbund, 'rU') if isinstance(args.strFileAbund,str) else args.strFileAbund, delimiter="\t")
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89
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90 if args.strX is None:
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91 args.strX = strFeatureOneID
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92
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93 if args.strY is None:
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94 args.strY = strFeatureTwoID
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95
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96 # Get values and groupings
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97 for lsLine in csvReader:
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98 if lsLine[0] == strFeatureOneID:
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99 lxVariable1 = lsLine[1:]
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100 if not strFeatureTwoID is None:
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101 if lsLine[0] == strFeatureTwoID:
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102 lxVariable2 = lsLine[1:]
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103
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104 # Remove NAs
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105 liNAs = [i for i,x in enumerate(lxVariable1) if x.lower() == "na"]
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106 liNAs = set([i for i,x in enumerate(lxVariable1) if x.lower() == "na"]+liNAs)
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107 lxVariable1 = [x for i,x in enumerate(lxVariable1) if not i in liNAs]
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108
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109 if not lxVariable2 is None:
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110 lxVariable2 = [x for i,x in enumerate(lxVariable2) if not i in liNAs]
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111
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112 # Type variables
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113 if not lxVariable1 is None:
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114 try:
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115 float(lxVariable1[0])
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116 lxVariable1 = [float(xItem) for xItem in lxVariable1]
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117 fOneIsNumeric = True
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118 except ValueError:
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119 pass
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120
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121 if not lxVariable2 is None:
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122 try:
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123 float(lxVariable2[0])
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124 lxVariable2 = [float(xItem) for xItem in lxVariable2]
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125 fTwoIsNumeric = True
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126 except ValueError:
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127 pass
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128
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129 if lxVariable1 is None:
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130 print("scriptPlotFeature:: Sorry, could not find the feature "+ strFeatureOneID +" in the file "+args.strFileAbund+" .")
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131 elif( (lxVariable2 is None) and (not strFeatureTwoID is None) ):
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132 print("scriptPlotFeature:: Sorry, could not find the feature "+ strFeatureTwoID +" in the file "+args.strFileAbund+" .")
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133 else:
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134 # Plot as needed
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135 if((not lxVariable1 is None ) and (not lxVariable2 is None)):
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136 if(sum([fOneIsNumeric, fTwoIsNumeric])==0):
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137 print "scriptPlotFeature:: Error, If plotting 2 variables, atleast 1 should be numeric."
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138 elif(sum([fOneIsNumeric, fTwoIsNumeric])==1):
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139 funcPlotBoxPlot(lxVariable1,lxVariable2, fOneIsNumeric=fOneIsNumeric)
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140 elif(sum([fOneIsNumeric, fTwoIsNumeric])==2):
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141 ScatterPlot.funcPlot(lxVariable1, lxVariable2, args.strOutputFile, strTitle=args.strTitle, strXTitle=args.strX, strYTitle=args.strY, strColor=args.strColor, fInvert=args.fColor)
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142 elif(not lxVariable1 is None ):
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143 if fOneIsNumeric:
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144 Histogram.funcPlot(lxVariable1, args.strOutputFile, strTitle=args.strTitle, strXTitle=args.strX, strYTitle="Frequency", strColor=args.strColor, fInvert=args.fColor)
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145 else:
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146 print "Sorry currently histograms are support for only numeric data."
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