| browseMotifs {motifStack} | R Documentation |
browse motifs in a web browser
browseMotifs(pfms, phylog,
layout=c("tree", "cluster", "radialPhylog"),
nodeRadius=2.5, baseWidth=12, baseHeight=30,
xaxis=TRUE, yaxis=TRUE,
width=NULL, height=NULL,
...)
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 |
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.
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)