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$") #####Clustering##### hc <- clusterMotifs(pcms) ##reorder the motifs for plotMotifLogoStack motifs<-pcms[hc$order] motifs <- lapply(motifs, pcm2pfm) ##do alignment motifs<-DNAmotifAlignment(motifs) ##plot stacks plotMotifLogoStack(motifs, ncex=1.0) plotMotifLogoStackWithTree(motifs, hc=hc)