browseMotifs {motifStack} | R Documentation

## browse motifs

### Description

browse motifs in a web browser

### Usage

    browseMotifs(pfms, phylog,
                          layout=c("tree", "cluster", "radialPhylog"),
                          nodeRadius=2.5, baseWidth=12, baseHeight=30,
                          xaxis=TRUE, yaxis=TRUE,
                          width=NULL, height=NULL,
                          ...)

### Arguments

`pfms` | a list of pfm
`phylog` | layout type. see GraphvizLayouts
`layout` | layout type. Could be tree, cluster or radialPhylog.
`nodeRadius` | node radius, default 2.5px.
`baseWidth,baseHeight` | width and height of each alphabet of the motif logo.
`xaxis,yaxis` | plot x-axis or y-axis or not in the motifs.
`width` | width of the figure
`height` | height of the figure
`...` | parameters not used

### Value

An object of class htmlwidget that will intelligently print itself into HTML in a variety of contexts including the R console, within R Markdown documents, and within Shiny output bindings.

### Examples

    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, 10)
    pfms <- lapply(names(pfms), function(.ele, pfms){new("pfm",mat=pfms[[.ele]], name=.ele)},pfms)
    browseMotifs(pfms)

[Package motifStack version 1.31.2 Index]