def enrich(self):
"""
check for annotation enrichment for selected sequences (compared to other sequences in this experiment)
"""
if not self.cexp.cdb:
hs.Debug(8,'No cooldb loaded')
return
selseqs=[]
for cid in self.selection:
selseqs.append(self.cexp.seqs[cid])
bmd=hs.cooldb.testenrichment(self.cexp.cdb,self.cexp.seqs,selseqs)
hs.Debug(6,'found %d items' % len(bmd))
if len(bmd)>0:
slistwin = SListWindow(listname='Enrichment')
bmd=hs.sortenrichment(bmd)
for cbmd in bmd:
if cbmd['observed']<cbmd['expected']:
ccolor=QtGui.QColor(155,0,0)
else:
ccolor=QtGui.QColor(0,155,0)
item = QtGui.QListWidgetItem()
item.setText("%s (p:%f o:%d e:%f)" % (cbmd['description'],cbmd['pval'],cbmd['observed'],cbmd['expected']))
item.setTextColor(ccolor)
slistwin.lList.addItem(item)
print("%s (p:%f o:%d e:%f)" % (cbmd['description'],cbmd['pval'],cbmd['observed'],cbmd['expected']))
slistwin.exec_()
def bicluster(self):
newexp, seqs, samples = hs.bicluster(self.cexp, method="binary", sampkeep=0, bactkeep=0, justcount=True)
self.samples = samples[0]
self.seqs = seqs[0]
self.lNumSamples.setText(str(len(self.samples)))
self.lNumBacteria.setText(str(len(self.seqs)))
self.lSamples.clear()
self.lBacteria.clear()
# get the new bacteria and sample order
allsamp = np.arange(len(self.cexp.samples))
allbact = np.arange(len(self.cexp.seqs))
x = np.setdiff1d(allsamp, self.samples)
sampo = np.concatenate((self.samples, x))
ubact = []
for cseq in self.seqs:
ubact.append(self.cexp.seqdict[cseq])
bacto = np.concatenate((ubact, np.setdiff1d(allbact, ubact)))
self.cexp.bactorder = bacto
self.cexp.samporder = sampo
# if we have enough bacteria and samples, update the info list
if len(self.seqs) >= 5 and len(self.samples) >= 5:
sampmd = hs.testmdenrichmentall(self.cexp, self.samples)
for cmd in sampmd:
if cmd["observed"] < cmd["expected"]:
ccolor = QtGui.QColor(155, 0, 0)
else:
ccolor = QtGui.QColor(0, 155, 0)
item = QtWidgets.QListWidgetItem()
item.setText(
"%s - %s (p:%f o:%d e:%f)"
% (cmd["field"], cmd["val"], cmd["pval"], cmd["observed"], cmd["expected"])
)
item.setForeground(ccolor)
self.lSamples.addItem(item)
if self.cooldb:
bmd = hs.annotationenrichment(self.cexp, self.seqs)
# bmd=hs.cooldb.testenrichment(self.cooldb,self.cexp.seqs,self.seqs)
bmd = hs.sortenrichment(bmd)
for cbmd in bmd:
if cbmd["observed"] < cbmd["expected"]:
ccolor = QtGui.QColor(155, 0, 0)
else:
ccolor = QtGui.QColor(0, 155, 0)
item = QtWidgets.QListWidgetItem()
item.setText(
"%s (p:%f o:%d e:%f)" % (cbmd["description"], cbmd["pval"], cbmd["observed"], cbmd["expected"])
)
item.setForeground(ccolor)
self.lBacteria.addItem(item)
def enrichment(self):
items=self.bMainList.selectedItems()
if len(items)!=1:
print("Need 1 item")
return
for citem in items:
cname=str(citem.text())
cexp=self.explist[cname]
if self.cooldb:
evals=hs.cooldb.testenrichment(self.cooldb,[],cexp.seqs,freqs=np.log(1+np.mean(cexp.data,axis=1)))
# sevals=hs.sortenrichment(evals,method='val')
sevals=hs.sortenrichment(evals,method='single',epsilon=1)
for cval in sevals[::-1]:
print('%s - obs:%f catfreq:%f' % (cval['description'],cval['observed'],cval['expected']))