plot sequence logo stacks with a ape4-style phylogenic tree

Description

plot sequence logo stacks with a ape4-style phylogenic tree

Usage

plotMotifStackWithPhylog(phylog, pfms=NULL,
                         f.phylog = 0.3, f.logo = NULL, cleaves =1, cnodes =0,
                         labels.leaves = names(phylog$leaves), clabel.leaves=1,
                         labels.nodes = names(phylog$nodes), clabel.nodes = 0, 
                         font="Helvetica-Bold", ic.scale=TRUE, fontsize=12)

Arguments

Value

none

See Also

plot.phylog

Examples

  if(interactive()){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    jaspar.scores <- MotIV::readDBScores(file.path(find.package("MotIV"), 
                                    "extdata", "jaspar2010_PCC_SWU.scores"))
    d <- MotIV::motifDistances(lapply(pfms, pfm2pwm))
    hc <- MotIV::motifHclust(d, method="average")
    phylog <- hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- lapply(names(pfms), function(.ele, pfms){new("pfm",mat=pfms[[.ele]], 
                                                     name=.ele)},pfms)
    pfms <- DNAmotifAlignment(pfms, minimalConsensus=3)
    plotMotifStackWithPhylog(phylog, pfms, f.phylog=0.3, 
                             cleaves = 0.5, clabel.leaves = 0.7)
  }

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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> 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/plotMotifStackWithPhylog.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotMotifStackWithPhylog
> ### Title: plot sequence logo stacks with a ape4-style phylogenic tree
> ### Aliases: plotMotifStackWithPhylog
> 
> ### ** Examples
> 
> #  if(interactive()){
>     library("MotifDb")
See system.file("LICENSE", package="MotifDb") for use restrictions.
>     matrix.fly <- query(MotifDb, "Dmelanogaster")
>     motifs <- as.list(matrix.fly)
>     motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", names(motifs), fixed=TRUE)]
>     names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
+                 gsub("_FBgn[0-9]+$", "", 
+                   gsub("[^a-zA-Z0-9]","_", 
+                      gsub("(_[0-9]+)+$", "", names(motifs)))))
>     motifs <- motifs[unique(names(motifs))]
>     pfms <- sample(motifs, 50)
>     jaspar.scores <- MotIV::readDBScores(file.path(find.package("MotIV"), 
+                                     "extdata", "jaspar2010_PCC_SWU.scores"))
>     d <- MotIV::motifDistances(lapply(pfms, pfm2pwm))
>     hc <- MotIV::motifHclust(d, method="average")
>     phylog <- hclust2phylog(hc)
>     leaves <- names(phylog$leaves)
>     pfms <- pfms[leaves]
>     pfms <- lapply(names(pfms), function(.ele, pfms){new("pfm",mat=pfms[[.ele]], 
+                                                      name=.ele)},pfms)
>     pfms <- DNAmotifAlignment(pfms, minimalConsensus=3)
>     plotMotifStackWithPhylog(phylog, pfms, f.phylog=0.3, 
+                              cleaves = 0.5, clabel.leaves = 0.7)
> #  }
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>