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Last data update: 2014.03.03 |
plot sequence logo stacks with a linear phylogenic tree and multiple color setsDescriptionplot sequence logo stacks with a linear phylogenic tree and multiple color sets. Usage
motifPiles(phylog, pfms=NULL, pfms2=NULL,
r.tree=.45, col.tree=NULL,
cnodes=0, labels.nodes=names(phylog$nodes), clabel.nodes=0,
cleaves=.2, labels.leaves=names(phylog$leaves), clabel.leaves=1,
col.leaves=rep("black", length(labels.leaves)),
col.leaves.bg=NULL, col.leaves.bg.alpha=1,
r.pfms=NA, r.pfms2=NA, motifScale=c("logarithmic", "linear"),
col.pfms=NULL, col.pfms.width=0.02,
col.pfms2=NULL, col.pfms2.width=0.02,
r.anno=0, col.anno=list(),
pfmNameSpliter=";", rcpostfix="(RC)", ic.scale=TRUE,
plotIndex=FALSE, IndexCol="black", IndexCex=.8,
groupDistance=NA, groupDistanceLineCol="red")
Arguments
Valuenone Author(s)Jianhong Ou See Also
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)
library(RColorBrewer)
color <- brewer.pal(12, "Set3")
motifPiles(phylog, pfms, cleaves = 0.5, clabel.leaves = 0.7,
col.leaves=rep(color, each=5),
col.leaves.bg = sample(colors(), 50),
col.tree=rep(color, each=5),
r.anno=c(0.02, 0.03, 0.04),
col.anno=list(sample(colors(), 50),
sample(colors(), 50),
sample(colors(), 50)))
}
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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> 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/motifPiles.Rd_%03d_medium.png", width=480, height=480)
> ### Name: motifPiles
> ### Title: plot sequence logo stacks with a linear phylogenic tree and
> ### multiple color sets
> ### Aliases: motifPiles
> ### Keywords: misc
>
> ### ** 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)
> library(RColorBrewer)
> color <- brewer.pal(12, "Set3")
> motifPiles(phylog, pfms, cleaves = 0.5, clabel.leaves = 0.7,
+ col.leaves=rep(color, each=5),
+ col.leaves.bg = sample(colors(), 50),
+ col.tree=rep(color, each=5),
+ r.anno=c(0.02, 0.03, 0.04),
+ col.anno=list(sample(colors(), 50),
+ sample(colors(), 50),
+ sample(colors(), 50)))
> # }
>
>
>
>
>
> dev.off()
null device
1
>
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