motifPiles: plot sequence logo stacks with a linear phylogenic tree and...

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

plot sequence logo stacks with a linear phylogenic tree and multiple color sets

Description

plot sequence logo stacks with a linear phylogenic tree and multiple color sets.

Usage

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"
)

Arguments

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

Value

none

Author(s)

Jianhong Ou

See Also

motifCircos

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")
    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)))
  }

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