motifStack (version 1.16.2)

plotMotifLogoStackWithTree: 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$")
  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)