plotMotifStackWithRadialPhylog: plot sequence logo stacks with a radial phylogenic tree

In jianhong/motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

plot sequence logo stacks with a radial phylogenic tree

Description

plot sequence logo stacks with a radial phylogenic tree

Usage

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 = 0.8,
  groupDistance = NA,
  groupDistanceLineCol = "red",
  plotAxis = FALSE,
  font = "sans",
  ...
)

Arguments

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
...	not used.

Value

none

See Also

plot.phylog

Examples

  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")
    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))
  }

jianhong/motifStack documentation built on Jan. 31, 2024, 5:03 a.m.