plotMotifLogoStackWithTree: plot sequence logos stack with hierarchical cluster tree

In motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

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)

motifStack documentation built on Nov. 8, 2020, 7:43 p.m.