viewTracks {trackViewer} | R Documentation |
A function to plot the data for given range
viewTracks( trackList, chromosome, start, end, strand, gr = GRanges(), ignore.strand = TRUE, viewerStyle = trackViewerStyle(), autoOptimizeStyle = FALSE, newpage = TRUE, operator = NULL, smooth = FALSE )
trackList |
an object of |
chromosome |
chromosome |
start |
start position |
end |
end position |
strand |
strand |
gr |
an object of |
ignore.strand |
ignore the strand or not when do filter. default TRUE |
viewerStyle |
an object of |
autoOptimizeStyle |
should use |
newpage |
should be draw on a new page? |
operator |
operator, could be +, -, *, /, ^, %%. "-" means dat - dat2, and so on. |
smooth |
logical(1) or numeric(1). Smooth the curve or not. If it is numeric, eg n, mean of nearby n points will be used for plot. |
An object of viewport
for addGuideLine
See Also as addGuideLine
, addArrowMark
extdata <- system.file("extdata", package="trackViewer", mustWork=TRUE) files <- dir(extdata, "-.wig") tracks <- lapply(paste(extdata, files, sep="/"), importScore, format="WIG") tracks <- lapply(tracks, function(.ele) {strand(.ele@dat) <- "-"; .ele}) fox2 <- importScore(paste(extdata, "fox2.bed", sep="/"), format="BED") dat <- coverageGR(fox2@dat) fox2@dat <- dat[strand(dat)=="+"] fox2@dat2 <- dat[strand(dat)=="-"] gr <- GRanges("chr11", IRanges(122929275, 122930122), strand="-") viewTracks(trackList(track=tracks, fox2=fox2), gr=gr, autoOptimizeStyle=TRUE)