try:
from rpy2 import robjects as ro
r = ro.r
except ImportError:
ro = None
r = None
def asdict(x, defaults=None):
if defaults is None:
defaults = {}
if x is None:
return defaults
defaults.update(x)
return defaults
def ecdf(vectors, labels=None, colors=["red", "blue", "orange", "violet", "green", "brown"],
xlab="", ylab="cumulative fraction", main="", legendWhere="topleft",
lty=1, lwd=1, legendArgs=None, labelsIncludeN=True, **ecdfKwdArgs):
""" Take a list of lists, convert them to vectors, and plots them sequentially on a CDF """
if ro is None:
return
#print "MEANS:", main
#for vector, label in zip(convertToVectors, labels):
# print label, numpy.mean(vector)
def _expand(item):
try:
iter(item)
return item
except TypeError:
return [item] * len(vectors)
lty = _expand(lty)
lwd = _expand(lwd)
if not "xlim" in ecdfKwdArgs or ecdfKwdArgs["xlim"] is None:
xlim = [min(min(vector) for vector in vectors if len(vector) > 0),
max(max(vector) for vector in vectors if len(vector) > 0)]
ecdfKwdArgs["xlim"] = xlim
ecdfKwdArgs["xlim"] = ro.FloatVector(ecdfKwdArgs["xlim"])
started = False
for i, vector in enumerate(vectors):
if len(vector) > 0:
vector = ro.FloatVector(vector)
ecdfKwdArgs.update({"verticals":True, "do.points":False,
"col.hor":colors[(i)%len(colors)],
"col.vert":colors[(i)%len(colors)],
"lty":lty[(i)%len(lty)],
"lwd":lwd[(i)%len(lwd)]})
ecdf = r.ecdf(vector)
if not started:
r.plot(ecdf, main=main, xlab=xlab, ylab=ylab, **ecdfKwdArgs)
started = True
else:
r.plot(ecdf, add=True, **ecdfKwdArgs)
if labels is not None:
if labelsIncludeN:
labelsWithN = []
for i, label in enumerate(labels):
labelsWithN.append(label+" (n=%d)"%len(vectors[i]))
else:
labelsWithN = labels
legendArgs = asdict(legendArgs, {"cex":0.7})
r.legend(legendWhere, legend=ro.StrVector(labelsWithN), lty=ro.IntVector(lty),
lwd=ro.IntVector([lwdi*2 for lwdi in lwd]), col=ro.StrVector(colors),
bg="white", **legendArgs)
def barPlot(dict_, keysInOrder=None, printCounts=True, ylim=None, *args, **kwdargs):
""" Plot a bar plot
Args:
dict_: a dictionary of name -> value, where value is the height of the bar
use a collections.OrderedDict() to easily convey the order of the groups
keysInOrder: an optional ordering of the keys in dict_ (alternate option to using collections.OrderedDict)
printCounts: option to print the counts on top of each bar
additional kwdargs are passed directly to r.barplot()
"""
if not keysInOrder:
keysInOrder = dict_.keys()
heights = ro.FloatVector([dict_[key] for key in keysInOrder])
kwdargs["names.arg"] = ro.StrVector(keysInOrder)
if ylim is None:
if printCounts:
ylim = [min(heights), max(heights)*1.1]
else:
ylim = [min(heights), max(heights)]
x = r.barplot(heights, ylim=ro.FloatVector(ylim), *args, **kwdargs)
if printCounts:
heightsStrings = ["{:.2g}".format(height) for height in heights]
r.text(x, ro.FloatVector(heights), ro.StrVector(heightsStrings), pos=3)
return x
