| plotMotifLogoStackWithTree {motifStack} | R Documentation |
plot sequence logos stack with hierarchical cluster tree
plotMotifLogoStackWithTree(pfms, hc, treewidth=1/8, trueDist=FALSE, ...)
pfms |
a list of position frequency matrices, pfms must be a list of class pfm |
hc |
an object of the type produced by stats::hclust |
treewidth |
the width to show tree |
trueDist |
logical flags to use hclust height or not. |
... |
other parameters can be passed to plotMotifLogo function |
none
#####Input#####
pcms<-readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")
motifs<-lapply(pcms,pcm2pfm)
#####Clustering#####
jaspar.scores <- MotIV::readDBScores(file.path(find.package("MotIV"),
"extdata", "jaspar2010_PCC_SWU.scores"))
d <- MotIV::motifDistances(lapply(motifs, pfm2pwm))
hc <- MotIV::motifHclust(d, method="average")
##reorder the motifs for plotMotifLogoStack
motifs<-motifs[hc$order]
##do alignment
motifs<-DNAmotifAlignment(motifs)
##plot stacks
plotMotifLogoStack(motifs, ncex=1.0)
plotMotifLogoStackWithTree(motifs, hc=hc)