--- /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())