a character size for plotting the points that represent the leaves, used with par("cex")*cleaves. If zero, no points are drawn
cnodes
a character size for plotting the points that represent the nodes, used with par("cex")*cnodes. If zero, no points are drawn
labels.leaves
a vector of strings of characters for the leaves labels
clabel.leaves
a character size for the leaves labels, used with
labels.nodes
a vector of strings of characters for the nodes labels
clabel.nodes
a character size for the nodes labels, used with par("cex")*clabel.nodes. If zero, no nodes labels are drawn
draw.box
if TRUE draws a box around the current plot with the function box()
col.leaves
a vector of colors for leaves labels
col.leaves.bg
a vector of colors for background of leaves labels
col.leaves.bg.alpha
alpha value [0, 1] for the colors of backgroud of leaves labels
col.bg
a vector of colors for tree background
col.bg.alpha
a alpha value [0, 1] of colors for tree background
col.inner.label.circle
a vector of colors for inner cirlce of pfms
inner.label.circle.width
width for inner circle of pfms
col.outer.label.circle
a vector of colors for outer circle of pfms
outer.label.circle.width
width for outer circle of pfms
clockwise
a logical value indicating if slices are drawn clockwise or counter clockwise
init.angle
number specifying the starting angle (in degrees) for the slices. Defaults to 0 (i.e., ‘3 o’clock‘) unless clockwise is true where init.angle defaults to 90 (degrees), (i.e., '12 o’clock')
angle
number specifying the angle (in degrees) for phylogenic tree. Defaults 360
pfmNameSpliter
spliter when name of pfms contain multiple node of labels.leaves
rcpostfix
the postfix for reverse complements
motifScale
the scale of logo size
ic.scale
logical. If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.
plotIndex
logical. If TRUE, will plot index number in the motifLogo which can help user to describe the motifLogo
IndexCol
The color of the index number when plotIndex is TRUE.
IndexCex
The cex of the index number when plotIndex is TRUE.
groupDistance
show groupDistance on the draw
groupDistanceLineCol
groupDistance line color, default: red
plotAxis
logical. If TRUE, will plot distance axis.
font
font of logo
fontsize
font size of the template for grImport, default 12. Higher value make better quality figure, but also increase the file size.
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/plotMotifStackWithRadialPhylog.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotMotifStackWithRadialPhylog
> ### Title: plot sequence logo stacks with a radial phylogenic tree
> ### Aliases: plotMotifStackWithRadialPhylog
>
> ### ** 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(pfms)
> 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")
> plotMotifStackWithRadialPhylog(phylog, pfms, circle=0.9,
+ cleaves = 0.5, clabel.leaves = 0.7,
+ col.bg=rep(color, each=5), col.leaves=rep(color, each=5))
> # }
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.