plotMotifLogoStackWithTree {motifStack} | R Documentation

## plot sequence logos stack with hierarchical cluster tree

### Description

plot sequence logos stack with hierarchical cluster tree

### Usage

    plotMotifLogoStackWithTree(pfms, hc, treewidth = 1/8, trueDist = FALSE, ...)

### Arguments

`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

### Value

none

### Examples

      #####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)

[Package motifStack version 1.34.0 Index]