plotMotifStackWithRadialPhylog {motifStack} | R Documentation |
plot sequence logo stacks with a radial phylogenic tree
plotMotifStackWithRadialPhylog(phylog, pfms=NULL, circle=0.75, circle.motif=NA, cleaves=1, cnodes=0, labels.leaves=names(phylog$leaves), clabel.leaves=1, labels.nodes=names(phylog$nodes), clabel.nodes=0, draw.box=FALSE, col.leaves=rep("black", length(labels.leaves)), col.leaves.bg=NULL, col.leaves.bg.alpha=1, col.bg=NULL, col.bg.alpha=1, col.inner.label.circle=NULL, inner.label.circle.width="default", col.outer.label.circle=NULL, outer.label.circle.width="default", clockwise =FALSE, init.angle=if(clockwise) 90 else 0, angle=360, pfmNameSpliter=";", rcpostfix = "(RC)", motifScale=c("linear","logarithmic"), ic.scale=TRUE, plotIndex=FALSE, IndexCol="black", IndexCex=.8, groupDistance=NA, groupDistanceLineCol="red", plotAxis=FALSE, font="Helvetica-Bold", fontsize=12)
phylog |
an object of class phylog |
pfms |
a list of objects of class pfm |
circle |
a size coefficient for the outer circle of the labels. Please note this is the position of inner.label.cirle. |
circle.motif |
a size coefficient for the motif circle |
cleaves |
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 par("cex")*clabel.leaves |
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. |
none
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(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)) }