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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(motifStack)
Loading required package: grImport
Loading required package: grid
Loading required package: XML
Loading required package: MotIV
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'MotIV'

The following object is masked from 'package:stats':

    filter

Loading required package: ade4

Attaching package: 'ade4'

The following object is masked from 'package:BiocGenerics':

    score

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/motifStack/plotMotifLogoStackWithTree.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotMotifLogoStackWithTree
> ### Title: plot sequence logos stack with hierarchical cluster tree
> ### Aliases: plotMotifLogoStackWithTree
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>