def simpleheatmap(tabdata, figname='defaultheatplot.pdf', main='title',
colormode='jet', gformat='pdf', scale='none', dendrogram='both'):
"""
scale: none, row, both, col
"""
rconsole = rpy2.robjects.r
rsimpleheatmap = rconsole("rsimpleheatmap")
dopdfgraph = rconsole("dopdfgraph")
rdataframe = pyobj2dataframe(tabdata, rownames=True, columnames=True)
from rpy2.robjects.packages import importr
grdevices = importr('grDevices')
grdevices.pdf(file=fhutils.renamefilename(figname, suffix=gformat))
roworder = {'both': True, 'row': True, 'column': False}[dendrogram]
colorder = {'both': True, 'row': False, 'column': True}[dendrogram]
rsimpleheatmap(tabdata=rdataframe, scale=scale, dendros=dendrogram, roworder=roworder, colorder=colorder)
grdevices.dev_off()
def setupdata(tabdata, doscale, group, error, dofit=None):
if doscale:
doscale = rpy2.robjects.vectors.FloatVector(tuple(doscale))
if group in ('', 'NA', '1'):
group = rinterface.NACharacterType()
elif isinstance(group, tuple) or isinstance(group, list):
group = rpy2.robjects.vectors.StrVector(list(group))
tabdata, group = fusegroupcolumns(tabdata, group)
if isinstance(dofit, tuple):
dofit = rpy2.robjects.vectors.StrVector(tuple(dofit))
else:
dofit = rpy2.robjects.vectors.StrVector(tuple((0, 0)))
if error in ('', 'NA'):
error = rinterface.NACharacterType()
dataframe = pyobj2dataframe(tabdata)
return dataframe, doscale, group, error, dofit
