In jianhong/trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

suppressPackageStartupMessages({
    library(trackViewer)
    library(rtracklayer)
    library(Gviz)
    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
    library(org.Hs.eg.db)
    library(VariantAnnotation)
  library(httr)
})
knitr::opts_chunk$set(warning=FALSE, message=FALSE)

• Plot methylation/mutation/variant data by lollipop plot

• Plot high dense methylation/mutation/variant data by dandelion plot

• Plot genomic interaction data (HiC, cooler, etc) by viewTracks

Prepare toy data

First, we import the sample data.

library(trackViewer)
extdata <- system.file("extdata", package="trackViewer",
                       mustWork=TRUE)
repA <- importScore(file.path(extdata, "cpsf160.repA_-.wig"),
                    file.path(extdata, "cpsf160.repA_+.wig"),
                    format="WIG")
## Because the wig file does not contain any strand info, 
## we need to set it manually.
strand(repA$dat) <- "-"
strand(repA$dat2) <- "+"

fox2 <- importScore(file.path(extdata, "fox2.bed"), format="BED",
                    ranges=GRanges("chr11", IRanges(122830799, 123116707)))
dat <- coverageGR(fox2$dat)
## We can split the data by strand into two different track channels
## Here, we set the dat2 slot to save the negative strand info. 

fox2$dat <- dat[strand(dat)=="+"]
fox2$dat2 <- dat[strand(dat)=="-"]

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
gr <- GRanges("chr11", IRanges(122929275, 122930122), strand="-")
trs <- geneModelFromTxdb(TxDb.Hsapiens.UCSC.hg19.knownGene,
                         org.Hs.eg.db,
                         gr=gr)

optSty <- optimizeStyle(trackList(repA, fox2, trs))
trackList <- optSty$tracks
viewerStyle <- optSty$style

Using the browseTracks function as a helper

Since version 1.33.6, the interactive plot generated by browseTracks function will print the psuedocode about how to change the track styles at the bottom, which can be used as a quick reference.

browseTracks(trackList, gr=gr)

\ \

Adjust the x-axis or the X scale

In most cases, researchers are interested in the relative position of the peaks in the gene. Sometimes, margin needs to be adjusted to be able to show the entire gene model. The Figure below shows how to add an X scale (x-scale) and remove the x-axis using the setTrackXscaleParam and setTrackViewerStyleParam functions.

setTrackViewerStyleParam(viewerStyle, "xaxis", FALSE)
setTrackViewerStyleParam(viewerStyle, "margin", c(.01, .05, .01, .01))
setTrackXscaleParam(trackList[[1]], "draw", TRUE)
setTrackXscaleParam(trackList[[1]], "gp", list(cex=0.8))
viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)
setTrackXscaleParam(trackList[[1]], attr="position", 
                    value=list(x=122929700, y=3, label=200))
viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

Adjust the y-axis

The y-axis can be put to the right side of the track by setting the main slot to FALSE in the y-axis slot of each track. In addition, the limit of y-axis (ylim) can be set by setTrackStyleParam.

setTrackViewerStyleParam(viewerStyle, "margin", c(.01, .05, .01, .05))
for(i in 1:2){
    setTrackYaxisParam(trackList[[i]], "main", FALSE)
}
## Adjust the limit of y-axis
setTrackStyleParam(trackList[[1]], "ylim", c(0, 25))
setTrackStyleParam(trackList[[2]], "ylim", c(-25, 0))
## The y-axis tick labels can be turn off/on by setting the 'label' to FALSE/TRUE
#setTrackYaxisParam(trackList[[1]], 'label', TRUE)
viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

The function setTrackYaxisParam can be sued to adjust the track color/size/etc of y-axis and the y-axis labels.

## change the 
setTrackYaxisParam(trackList[[1]], "gp", list(cex=.8, col="green"))
setTrackYaxisParam(trackList[[2]], "gp", list(cex=.8, col="blue"))
viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

Adjust the label of y-axis

The style of y-axis can be changed by setting the ylabgp slot in the style of each track.

setTrackStyleParam(trackList[[1]], "ylabgp", list(cex=.8, col="green"))
## set cex to avoid automatic adjust
setTrackStyleParam(trackList[[2]], "ylabgp", list(cex=.8, col="blue"))
setTrackStyleParam(trackList[[2]], "marginBottom", .2)
viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

The y-axis label can be put at the top or the bottom of each track.

setTrackStyleParam(trackList[[1]], "ylabpos", "bottomleft")
setTrackStyleParam(trackList[[2]], "ylabpos", "topright")
setTrackStyleParam(trackList[[2]], "marginTop", .2)
viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

For each transcript, the transcript name can be put on the upstream or downstream of the transcript. The Y-lab can also be removed by set 'ylabpos' to 'none' or set the name as ''.

trackListN <- trackList
setTrackStyleParam(trackListN[[3]], "ylabpos", "upstream")
setTrackStyleParam(trackListN[[4]], "ylabpos", "downstream")
## set cex to avoid automatic adjust
setTrackStyleParam(trackListN[[3]], "ylabgp", list(cex=.6))
setTrackStyleParam(trackListN[[4]], "ylabgp", list(cex=.6))
## remove ylab
setTrackStyleParam(trackListN[[5]], "ylabpos", "none")
names(trackListN)[6] <- ""
gr1 <- range(unname(unlist(GRangesList(sapply(trs, function(.ele) .ele$dat)))))
start(gr1) <- start(gr1) - 2000
end(gr1) <- end(gr1) + 2000
viewTracks(trackListN, gr=gr1, viewerStyle=viewerStyle)

Adjust the track color

The track color can be changed by setting the color slot in the style of each track. The first color is for the dat slot of track and the second color is for the dat2 slot.

setTrackStyleParam(trackList[[1]], "color", c("green", "black"))
setTrackStyleParam(trackList[[2]], "color", c("black", "blue"))
for(i in 3:length(trackList)) 
    setTrackStyleParam(trackList[[i]], "color", "black")
viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

Adjust the track height

The track height can be changed by setting the height slot in the style of each track. However, the total height for all the tracks should be 1.

trackListH <- trackList
setTrackStyleParam(trackListH[[1]], "height", .1)
setTrackStyleParam(trackListH[[2]], "height", .44)
for(i in 3:length(trackListH)){
    setTrackStyleParam(trackListH[[i]], "height", 
                       (1-(0.1+0.44))/(length(trackListH)-2))
}
viewTracks(trackListH, gr=gr, viewerStyle=viewerStyle)

Change the track names

The track names such as gene model names can be edited easily by changing the names of trackList.

names(trackList) <- c("cpsf160", "fox2", rep("HSPA8", 5))
viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

Show paired data in the same track

trackViewer can be used to show to-be-compared data in the same track side by side.

cpsf160 <- importScore(file.path(extdata, "cpsf160.repA_-.wig"),
                       file.path(extdata, "cpsf160.repB_-.wig"),
                       format="WIG")
strand(cpsf160$dat) <- strand(cpsf160$dat2) <- "-"
setTrackStyleParam(cpsf160, "color", c("black", "red"))
viewTracks(trackList(trs, cpsf160), gr=gr, viewerStyle=viewerStyle)

Show signals and the called peaks

The called peaks can be plotted as annotation.

cpsf160_cp <- cpsf160
cpsf160$dat2 <- reduce(cpsf160$dat)
cpsf160$dat2$score <- sample.int(length(cpsf160$dat2))
setTrackStyleParam(cpsf160, "tracktype", c("peak", "annotation"))
cpsf160_cp$dat <- reduce(cpsf160_cp$dat2)
cpsf160_cp$dat$score <- sample.int(length(cpsf160_cp$dat))
setTrackStyleParam(cpsf160_cp, "tracktype", c("annotation", "peak"))
setTrackStyleParam(cpsf160_cp, "marginTop", 0.05)
viewTracks(trackList(trs, cpsf160, cpsf160_cp), gr=gr, viewerStyle=viewerStyle)

Flip the x-axis

The x-axis can be horizotally flipped for the genes in the negative strand.

viewerStyleF <- viewerStyle
setTrackViewerStyleParam(viewerStyleF, "flip", TRUE)
setTrackViewerStyleParam(viewerStyleF, "xaxis", TRUE)
setTrackViewerStyleParam(viewerStyleF, "margin", c(.1, .05, .01, .01))
vp <- viewTracks(trackList, gr=gr, viewerStyle=viewerStyleF)
addGuideLine(c(122929767, 122929969), vp=vp)
addArrowMark(list(x=122929650,
                  y=2),
             label="label",
             col="blue",
             vp=vp)

Optimize the theme

Currently, we support two themes: bw (black and white) and col (colored).

optSty <- optimizeStyle(trackList(repA, fox2, trs), theme="bw")
trackList <- optSty$tracks
viewerStyle <- optSty$style
vp <- viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

optSty <- optimizeStyle(trackList(repA, fox2, trs), theme="col")
trackList <- optSty$tracks
viewerStyle <- optSty$style
vp <- viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

optSty <- optimizeStyle(trackList(repA, fox2, trs), theme="safe")
trackList <- optSty$tracks
viewerStyle <- optSty$style
vp <- viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

Plot with breaks

We could plot the tracks with breaks by setting multiple genomic ranges.

gr.breaks <- GRanges("chr11", 
                     IRanges(c(122929275, 122929575, 122929775), 
                             c(122929555, 122929725, 122930122)), 
                     strand="-", percentage=c(.4, .2, .4))
vp <- viewTracks(trackList, gr=gr.breaks, viewerStyle=viewerStyle)

Session Info

sessionInfo()

jianhong/trackViewer documentation built on Jan. 3, 2025, 10:33 p.m.