import math, cmath
import sys
import optparse
+from commoncode import getConfigParser, getConfigOption, getConfigIntOption, getConfigFloatOption, getConfigBoolOption
alphaVal = 0.5
-print "%prog: version 3.1"
+print "scatterfields: version 3.2"
def main(argv=None):
if not argv:
usage = __doc__
- 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")
- parser.set_defaults(forcexmin=0.0, forceymin=0.0, forcexmax=-1, forceymax=-1, doLogF1=False,
- doLogF2=False, doArcsinh=False, fitOrder=1, base=10, markFile=None,
- foldChange=None, doRegression=True, plotLarge=False, markDiag=False,
- figtitle="", verbose=False)
-
+ parser = getParser(usage)
(options, args) = parser.parse_args(argv[1:])
if len(args) < 6:
options.markDiag, options.figtitle, options.verbose)
+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
+
+
def scatterfields(infilename, xaxis, xField, yaxis, yField, outfilename, forcexmin=0.0, forceymin=0.0,
forcexmax=-1, forceymax=-1, doLogF1=False, doLogF2=False, doArcsinh=False, fitOrder=1,
base=10, markFile=None, foldChange=None, doRegression=True, plotLarge=False,