plotMotifLogoStackWithTree: plot sequence logos stack with hierarchical cluster tree

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

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)

jianhong/motifStack documentation built on Jan. 31, 2024, 5:03 a.m.