Mercurial > repos > sagun98 > micropita
diff galaxy_micropita/src/breadcrumbs/src/BoxPlot.py @ 3:8fb4630ab314 draft default tip
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author | sagun98 |
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date | Thu, 03 Jun 2021 17:07:36 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_micropita/src/breadcrumbs/src/BoxPlot.py Thu Jun 03 17:07:36 2021 +0000 @@ -0,0 +1,130 @@ +""" +Author: Timothy Tickle +Description: Class to create box plots. +""" + +##################################################################################### +#Copyright (C) <2012> +# +#Permission is hereby granted, free of charge, to any person obtaining a copy of +#this software and associated documentation files (the "Software"), to deal in the +#Software without restriction, including without limitation the rights to use, copy, +#modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, +#and to permit persons to whom the Software is furnished to do so, subject to +#the following conditions: +# +#The above copyright notice and this permission notice shall be included in all copies +#or substantial portions of the Software. +# +#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, +#INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A +#PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +#HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION +#OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE +#SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +##################################################################################### + +__author__ = "Timothy Tickle" +__copyright__ = "Copyright 2012" +__credits__ = ["Timothy Tickle"] +__license__ = "MIT" +__maintainer__ = "Timothy Tickle" +__email__ = "ttickle@sph.harvard.edu" +__status__ = "Development" + +#External libraries +from ConstantsFiguresBreadCrumbs import ConstantsFiguresBreadCrumbs +import matplotlib.pyplot as plt +from pylab import * + +#Plots a matrix +class BoxPlot: + + @staticmethod + def funcPlot(ly, lsLabels, strOutputFigurePath, strTitle = "Title", strXTitle="X Axis", strYTitle="Y Axis", strColor = "#83C8F9", fJitter=False, fInvert=False, fInvertY=False): + """ + Plot a box plot with optional jittering. + + :params ly: List of y values + :type: List of doubles + :params lsLabels: List of labels (x tick lables) + :type: List string + :params strOutputFigurePath: File path to make figure + :type: String file path + :params strTitle: Title of figure + :type: String + :params strXTitle: Label of x axis + :type: String + :params strYTitle: Label of y axis + :type: String + :params strColor: Hex color for the face of the boxplots + :type: String + :params fJitter: Indicator of jittering (true) or not (false) + :type: Boolean + :params fInvert: Invert colors (true) + :type: Boolean + :params fInvertY: Invert y axis + :type: Boolean + """ + + #Start plot + #Get plot object + imgFigure = plt.figure() + + #Get plot colorsstrOutFigure + objFigureControl = ConstantsFiguresBreadCrumbs() + #Boxplots have to be plotted over the scatter so the alpha can not go to 1.0 + #In this case capturing the alpha before inversion + #Inversion automoatically sets it to 1. + dAlpha=objFigureControl.c_dAlpha + objFigureControl.invertColors(fInvert=fInvert) + + #Color/Invert figure + imgFigure.set_facecolor(objFigureControl.c_strBackgroundColorWord) + imgSubplot = imgFigure.add_subplot(111,axisbg=objFigureControl.c_strBackgroundColorLetter) + imgSubplot.set_xlabel(strXTitle) + imgSubplot.set_ylabel(strYTitle) + imgSubplot.spines['top'].set_color(objFigureControl.c_strDetailsColorLetter) + imgSubplot.spines['bottom'].set_color(objFigureControl.c_strDetailsColorLetter) + imgSubplot.spines['left'].set_color(objFigureControl.c_strDetailsColorLetter) + imgSubplot.spines['right'].set_color(objFigureControl.c_strDetailsColorLetter) + imgSubplot.xaxis.label.set_color(objFigureControl.c_strDetailsColorLetter) + + #Adds light grid for numbers and puts them in the background + imgSubplot.yaxis.grid(True, linestyle='-', which='major', color=objFigureControl.c_strGridLineColor, alpha=objFigureControl.c_dAlpha) + imgSubplot.set_axisbelow(True) + imgSubplot.yaxis.label.set_color(objFigureControl.c_strDetailsColorLetter) + imgSubplot.tick_params(axis='x', colors=objFigureControl.c_strDetailsColorLetter) + imgSubplot.tick_params(axis='y', colors=objFigureControl.c_strDetailsColorLetter) + charMarkerEdgeColor = objFigureControl.c_strDetailsColorLetter + + #Make box plot + bp = plt.boxplot(x=ly, notch=1, patch_artist=True) + for iindex, ldData in enumerate(ly): + ldX = None + if fJitter: + ldX = [float(iindex+1)+ uniform(-.05,.05) for x in xrange(len(ldData))] + else: + ldX = [float(iindex+1) for x in xrange(len(ldData))] + plt.scatter(x=ldX,y=ly[iindex],c=strColor,marker="o",alpha=objFigureControl.c_dAlpha) + + #Color boxes + plt.setp(bp['boxes'], color=objFigureControl.c_strDetailsColorLetter, facecolor=strColor, alpha=dAlpha) + plt.setp(bp['whiskers'], color=objFigureControl.c_strDetailsColorLetter) + + #Set ticks and title + lsLabelsWithCounts = [] + for iindex,sCurLabel in enumerate(lsLabels): + lsLabelsWithCounts.append(sCurLabel+" ( "+str(len(ly[iindex]))+" )") + xtickNames = plt.setp(imgSubplot, xticklabels=lsLabelsWithCounts) + imgSubplot.set_title(strTitle) + imgSubplot.title.set_color(objFigureControl.c_strDetailsColorLetter) + + #Invert Y axis + if fInvertY: + ax = plt.gca() + ax.set_ylim(ax.get_ylim()[::-1]) + + #End plot + #Save to a file + imgFigure.savefig(strOutputFigurePath, facecolor=imgFigure.get_facecolor())