motifCircos {motifStack} | R Documentation

## plot sequence logo stacks with a radial phylogenic tree and multiple color rings

### Description

plot sequence logo stacks with a radial phylogenic tree and multiple color rings. The difference from plotMotifStackWithRadialPhylog is that it has more color setting and one more group of pfms.

### Usage

    motifCircos(phylog, pfms=NULL, pfms2=NULL, R=2.5,
                r.tree=1, col.tree.bg=NULL, col.tree.bg.alpha=1,
                cnodes=0, labels.nodes=names(phylog$nodes), clabel.nodes=0,
                r.leaves=NA,
                cleaves=1, labels.leaves=names(phylog$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,
                r.rings=0, col.rings=list(),
                col.inner.label.circle=NULL, inner.label.circle.width=0.02,
                col.outer.label.circle=NULL, outer.label.circle.width=0.02,
                draw.box=FALSE,
                clockwise =FALSE, init.angle=if(clockwise) 90 else 0,
                angle=360, pfmNameSpliter=";", rcpostfix="(RC)",
                motifScale=c("linear","logarithmic","none"), ic.scale=TRUE,
                plotIndex=FALSE, IndexCol="black", IndexCex=.8,
                groupDistance=NA, groupDistanceLineCol="red",
                plotAxis=FALSE)

### Arguments

`phylog` | an object of class phylog
`pfms` | a list of objects of class pfm
`pfms2` | a list of objects of class pfm
`R` | radius of canvas
`r.tree` | half width of the tree
`col.tree.bg` | a vector of colors for tree background
`col.tree.bg.alpha` | a alpha value [0, 1] of colors for tree background
`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
`r.leaves` | width of the leaves
`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
`r.rings` | a vector of width of color rings
`col.rings` | a list of color rings
`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
`draw.box` | if TRUE draws a box around the current plot with the function box()
`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/pfms2 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.

### Value

none

### Author(s)

Jianhong Ou

### See Also

`plotMotifStackWithRadialPhylog`

### Examples

    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")
        motifCircos(phylog, pfms, cleaves = 0.5, clabel.leaves = 0.7,
                         col.tree.bg=rep(color, each=5), col.leaves=rep(color, each=5),
                          r.rings=c(0.02, 0.03, 0.04),
                          col.rings=list(sample(colors(), 50),
                                         sample(colors(), 50),
                                         sample(colors(), 50)))
      }

[Package motifStack version 1.28.0 Index]