motifPiles | R Documentation |
plot sequence logo stacks with a linear phylogenic tree and multiple color sets.
motifPiles(
phylog,
pfms = NULL,
pfms2 = NULL,
r.tree = 0.45,
col.tree = NULL,
cnodes = 0,
labels.nodes = names(phylog$nodes),
clabel.nodes = 0,
cleaves = 0.2,
labels.leaves = names(phylog$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", "none"),
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 = 0.8,
groupDistance = NA,
groupDistanceLineCol = "red"
)
phylog |
an object of class phylog |
pfms |
a list of objects of class pfm |
pfms2 |
a list of objects of class pfm |
r.tree |
width of the tree |
col.tree |
a vector of colors for tree |
cnodes |
a character size for plotting the points that represent the nodes, used with par("cex")*cnodes. If zero, no points are drawn |
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 |
cleaves |
a character size for plotting the points that represent the leaves, used with par("cex")*cleaves. 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 par("cex")*clavel.leaves |
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 |
r.pfms |
width of the pfms |
r.pfms2 |
width of the pfms2 |
motifScale |
the scale of logo size |
col.pfms |
a vector of colors for inner pile of pfms |
col.pfms.width |
width for inner pile of pfms |
col.pfms2 |
a vector of colors for outer pile of pfms |
col.pfms2.width |
width for outer pile of pfms |
r.anno |
a vector of width of color sets |
col.anno |
a list of color sets |
pfmNameSpliter |
spliter when name of pfms/pfms2 contain multiple node of labels.leaves |
rcpostfix |
the postfix for reverse complements |
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 |
none
Jianhong Ou
motifCircos
if(interactive() || Sys.getenv("USER")=="jianhongou"){
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)
hc <- clusterMotifs(pfms)
library(ade4)
phylog <- ade4::hclust2phylog(hc)
leaves <- names(phylog$leaves)
pfms <- pfms[leaves]
pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
new("pfm",mat=.ele, name=.name)})
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)))
}
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