Hello Jianhong,

I intended to create trackView on ChIPSeq data align with the peak. I did not find a function in trackViewer to import peak.narrowPeak file, so I did the following

library(GenomicRanges)
peaks.gr <- parse2GRanges("chr9:69035856-69037005:+")
values(peaks.gr) <- DataFrame(score = c(1))
peak <- new("track", dat = trackViewer:::orderedGR(peaks.gr), type = "data", format = "BED")

Then I performed plotting, however, the peaks are not shown as what I intended, which is similar to an IGV peak visualization, or the exon visualization in trackViewer.

Is there a way to visualize peaks easily in trackViewer, e.g. a function to import bed/narrowPeak/broadPeak files?

Thanks a lot!!

optSty <- optimizeStyle(trackList(HA1, HA2, genes, peak), theme="safe")
trackList <- optSty$tracks
viewerStyle <- optSty$style

setTrackViewerStyleParam(viewerStyle, "margin", c(.05, .2, .05, .05)) #bottom, left, top and right margin.
setTrackXscaleParam(trackList[[2]], "draw", TRUE)
setTrackXscaleParam(trackList[[2]], "gp", list(cex=0.8))
# setTrackXscaleParam(trackList[[2]], attr="position", 
#                     value=list(x=69035856, y=2, label=1000))
setTrackViewerStyleParam(viewerStyle, "xaxis", FALSE) # disable x ticks
setTrackStyleParam(trackList[[1]], "ylim", c(0, 0.5))
setTrackStyleParam(trackList[[2]], "ylim", c(0, 0.5))



vp <- viewTracks(trackList, 
                 gr=gr, viewerStyle=viewerStyle, 
                 autoOptimizeStyle=TRUE)

addGuideLine(c(69035856, 69037005), vp=vp) #peak1
addArrowMark(list(x=(69035856 + 69037005)/2,
                  y=2), # 2 means track 2 from the bottom.
             label="peak",
             col="darkgreen",
             vp=vp)

Hi,

Thanks for using trackViewer to plot your data. In current version of trackViewer, we don't have tracks for peak. There are two cheating methods you may want to try:

library(rtracklayer)
library(trackViewer)
extdata <- system.file("extdata", package="trackViewer",
mustWork=TRUE)
gr <- GRanges("chr11", IRanges(122929275, 122930122), strand="-")
fox2 <- importScore(file.path(extdata, "fox2.bed"), format="BED",
ranges=gr)
fox2$dat <- coverageGR(fox2$dat)
peaks <- GRanges("chr11", IRanges(c(122929350, 122929620, 122930050), width = 75), score=1)
## method 1, under the signal
fox2$dat2 <- peaks
## method 2, create a new track
peakTrack <- new("track", dat=peaks, type="data", format="BED")
## method 3, create a gene track
peaks$gene <- paste("peak", seq_along(peaks))
peaks$featureID <- peaks$gene
peaks$feature <- "CDS"
peakTrack2 <- new("track", dat=peaks, type="gene")
optSty <- optimizeStyle(trackList(fox2, peakTrack, peakTrack2,
                                  heightDist = c(10, .5, 1)), theme="safe")
trackList <- optSty$tracks
viewerStyle <- optSty$style
setTrackStyleParam(trackList[[1]], "color", c("brown", "green"))
viewTracks(trackList, gr=gr, viewerStyle = viewerStyle)

Jianhong.