+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--xmin", type="float", dest="forcexmin")
+ parser.add_option("--ymin", type="float", dest="forceymin")
+ parser.add_option("--xmax", type="float", dest="forcexmax")
+ parser.add_option("--ymax", type="float", dest="forceymax")
+ parser.add_option("--doLogF1", action="store_true", dest="doLogF1")
+ parser.add_option("--doLogF2", action="store_true", dest="doLogF2")
+ parser.add_option("--arcsinh", action="store_true", dest="doArcsinh")
+ parser.add_option("--order", type="int", dest="fitOrder")
+ parser.add_option("--base", type="int", dest="base")
+ parser.add_option("--markGenes", dest="markFile")
+ parser.add_option("--markfold", type="float", dest="foldChange")
+ parser.add_option("--noregression", action="store_false", dest="doRegression")
+ parser.add_option("--large", action="store_true", dest="plotLarge")
+ parser.add_option("--markdiag", action="store_true", dest="markDiag")
+ parser.add_option("--title", type="int", dest="figtitle")
+ parser.add_option("--verbose", action="store_true", dest="verbose")
+
+ configParser = getConfigParser()
+ section = "scatterfields"
+ forcexmin = getConfigFloatOption(configParser, section, "forcexmin", 0.0)
+ forceymin = getConfigFloatOption(configParser, section, "forceymin", 0.0)
+ forcexmax = getConfigIntOption(configParser, section, "forcexmax", -1)
+ forceymax = getConfigIntOption(configParser, section, "forceymax", -1)
+ doLogF1 = getConfigBoolOption(configParser, section, "doLogF1", False)
+ doLogF2 = getConfigBoolOption(configParser, section, "doLogF2", False)
+ doArcsinh = getConfigBoolOption(configParser, section, "doArcsinh", False)
+ fitOrder = getConfigIntOption(configParser, section, "fitOrder", 1)
+ base = getConfigIntOption(configParser, section, "base", 10)
+ markFile = getConfigOption(configParser, section, "markFile", None)
+ foldChange = getConfigOption(configParser, section, "foldChange", None)
+ doRegression = getConfigBoolOption(configParser, section, "doRegression", True)
+ plotLarge = getConfigBoolOption(configParser, section, "plotLarge", False)
+ markDiag = getConfigBoolOption(configParser, section, "markDiag", False)
+ figtitle = getConfigOption(configParser, section, "figtitle", "")
+ verbose = getConfigBoolOption(configParser, section, "verbose", False)
+
+ parser.set_defaults(forcexmin=forcexmin, forceymin=forceymin, forcexmax=forcexmax, forceymax=forceymax, doLogF1=doLogF1,
+ doLogF2=doLogF2, doArcsinh=doArcsinh, fitOrder=fitOrder, base=base, markFile=markFile,
+ foldChange=foldChange, doRegression=doRegression, plotLarge=plotLarge, markDiag=markDiag,
+ figtitle=figtitle, verbose=verbose)
+
+ return parser
+
+