motifPiles {motifStack} | R Documentation

## 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)))
      }

[Package motifStack version 1.38.0 Index]