motifPiles {motifStack} | R Documentation |
plot sequence logo stacks with a linear phylogenic tree and multiple color sets.
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", "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=.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
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))) }