## ----plotComp,echo=TRUE,fig.keep='none'----------------------------------
suppressPackageStartupMessages(library(Gviz))
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)

viewTracks(trackList(fox2), gr=gr, autoOptimizeStyle=TRUE, newpage=FALSE)

dt <- DataTrack(range=fox2$dat[strand(fox2$dat)=="-"] , 
                genome="hg19", type="hist", name="fox2", 
                window=-1, chromosome="chr11", 
                fill.histogram="black", col.histogram="NA",
                background.title="white",
                col.frame="white", col.axis="black",
                col="black", col.title="black")
plotTracks(dt, from=122929275, to=122930122, strand="-")

## ----Gviz,echo=FALSE,fig.cap='Plot data with **Gviz** and **trackViewer**. Note that **trackViewer** can generate similar figure as **Gviz** with several lines of simple codes.',fig.width=6,fig.height=1.5----
viewerStyle <- trackViewerStyle()
setTrackViewerStyleParam(viewerStyle, "margin", c(.01, .13, .02, .02))
empty <- DataTrack(showAxis=FALSE, showTitle=FALSE, background.title="white")
plotTracks(list(empty, dt), from=122929275, to=122930122, strand="-")
pushViewport(viewport(0, .5, 1, .5, just=c(0, 0)))
viewTracks(trackList(fox2), viewerStyle=viewerStyle, 
                 gr=gr, autoOptimizeStyle=TRUE, newpage=FALSE)
popViewport()
grid.text(label="Gviz track", x=.3, y=.4)
grid.text(label="trackViewer track", x=.3, y=.9)

## ----lostcode,echo=TRUE,fig.keep='none'----------------------------------
gr <- GRanges("chr1", IRanges(c(1, 6, 10), c(3, 6, 12)), score=c(3, 4, 1))
dt <- DataTrack(range=gr, data="score", type="hist")
plotTracks(dt, from=2, to=11)
tr <- new("track", dat=gr, type="data", format="BED")
viewTracks(trackList(tr), chromosome="chr1", start=2, end=11)

## ----GvizLost,echo=FALSE,fig.cap='Plot data with **Gviz** and **trackViewer**. Note that **trackViewer** is not only including more details but also showing all the data involved in the given range.',fig.width=6,fig.height=1.5----
plotTracks(list(empty, dt), from=2, to=11)
pushViewport(viewport(0, .5, 1, .5, just=c(0, 0)))
viewTracks(trackList(tr), viewerStyle=viewerStyle, 
           chromosome="chr1", start=2, end=11, 
           autoOptimizeStyle=TRUE, newpage=FALSE)
popViewport()
grid.text(label="Gviz track", x=.3, y=.4)
grid.text(label="trackViewer track", x=.3, y=.9)

## ----importData----------------------------------------------------------
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 strand info, 
## we need to set it manually
strand(repA$dat) <- "-"
strand(repA$dat2) <- "+"

## ----coverage------------------------------------------------------------
fox2 <- importScore(file.path(extdata, "fox2.bed"), format="BED",
                    ranges=GRanges("chr11", IRanges(122929000, 122931000)))
dat <- coverageGR(fox2$dat)
## we can split the data by strand into two different track channels
## here we set the dat2 slot to save the negative strand info, 
## reverse order as previous. 
fox2$dat <- dat[strand(dat)=="+"]
fox2$dat2 <- dat[strand(dat)=="-"]

## ----geneModel-----------------------------------------------------------
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
trs <- geneModelFromTxdb(TxDb.Hsapiens.UCSC.hg19.knownGene,
                         "chr11", 122929275, 122930122, "-")

## ----viewTracks,fig.cap='plot data and annotation information along genomic coordinates',fig.width=6,fig.height=1.5----
gr <- GRanges("chr11", IRanges(122929275, 122930122), strand="-")
viewerStyle <- trackViewerStyle()
setTrackViewerStyleParam(viewerStyle, "margin", c(.1, .05, .02, .02))
vp <- viewTracks(trackList(repA, fox2, trs), 
                 gr=gr, viewerStyle=viewerStyle, 
                 autoOptimizeStyle=TRUE)
addGuideLine(c(122929767, 122929969), vp=vp)
addArrowMark(list(x=122929650, 
                  y=unit(.39, "npc")),
             label="label",
             col="blue",
             vp=vp)

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

## ----viewTracksXaxis,fig.cap='plot data with x-scale',fig.width=6,fig.height=1.5----
setTrackViewerStyleParam(viewerStyle, "xaxis", FALSE)
setTrackViewerStyleParam(viewerStyle, "margin", c(.01, .05, .01, .01))
setTrackXscaleParam(trackList[[1]], "draw", TRUE)
setTrackXscaleParam(trackList[[1]], "gp", list(cex=.5))
viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

## ----viewTracksYaxis,fig.cap='plot data with y-axis in right side',fig.width=6,fig.height=1.5----
setTrackViewerStyleParam(viewerStyle, "margin", c(.01, .05, .01, .05))
setTrackYaxisParam(trackList[[1]], "main", FALSE)
setTrackYaxisParam(trackList[[2]], "main", FALSE)
viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

## ----viewTracksYlab,fig.cap='plot data with adjusted color and size of y label',fig.width=6,fig.height=1.5----
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)

## ----viewTracksYlabTopBottom,fig.cap='plot data with adjusted y label position',fig.width=6,fig.height=1.5----
setTrackStyleParam(trackList[[1]], "ylabpos", "bottomleft")
setTrackStyleParam(trackList[[2]], "ylabpos", "topright")
setTrackStyleParam(trackList[[2]], "marginTop", .2)
viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

## ----viewTracksYlabUpsDown,fig.cap='plot data with adjusted transcripts name position',fig.width=6,fig.height=1.5----
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))
gr1 <- range(unlist(GRangesList(sapply(trs, function(.ele) .ele$dat))))
start(gr1) <- start(gr1) - 2000
end(gr1) <- end(gr1) + 2000
viewTracks(trackListN, gr=gr1, viewerStyle=viewerStyle)

## ----viewTracksCol,fig.cap='plot data with adjusted track color',fig.width=6,fig.height=1.5----
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)

## ----viewTracksHeight,fig.cap='plot data with adjusted track height',fig.width=6,fig.height=1.5----
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)

## ----viewTracksNames,fig.cap='change the track names',fig.width=6,fig.height=1.5----
names(trackList) <- c("cpsf160", "fox2", rep("HSPA8", 5))
viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

## ----viewTracksPaired,fig.cap='show two data in the same track',fig.width=6,fig.height=1.2----
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)

## ----viewTracksFlipped,fig.cap='show data in the flipped track',fig.width=6,fig.height=2----
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=unit(.39, "npc")),
             label="label",
             col="blue",
             vp=vp)

## ----theme_bw,fig.cap='theme_bw',fig.width=6,fig.height=2----------------
optSty <- optimizeStyle(trackList(repA, fox2, trs), theme="bw")
trackList <- optSty$tracks
viewerStyle <- optSty$style
vp <- viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

## ----theme_col,fig.cap='theme_col',fig.width=6,fig.height=2--------------
optSty <- optimizeStyle(trackList(repA, fox2, trs), theme="col")
trackList <- optSty$tracks
viewerStyle <- optSty$style
vp <- viewTracks(trackList, gr=gr, viewerStyle=viewerStyle)

## ----viewTracksOperator1,fig.cap='show data with operator "+"',fig.width=6,fig.height=2----
newtrack <- repA
## must keep same format for dat and dat2
newtrack <- parseWIG(newtrack, "chr11", 122929275, 122930122)
newtrack$dat2 <- newtrack$dat
newtrack$dat <- fox2$dat2
setTrackStyleParam(newtrack, "color", c("blue", "red"))
viewTracks(trackList(newtrack, trs), 
           gr=gr, viewerStyle=viewerStyle, operator="+")

## ----viewTracksOperator2,fig.cap='show data with operator "-"',fig.width=6,fig.height=2----
viewTracks(trackList(newtrack, trs), gr=gr, viewerStyle=viewerStyle, operator="-")

## ----viewTracksOperator3,fig.cap='show data with operator "-"',fig.width=6,fig.height=2----
newtrack$dat <- GRoperator(newtrack$dat, newtrack$dat2, col="score", operator="-")
newtrack$dat2 <- GRanges()
viewTracks(trackList(newtrack, trs), gr=gr, viewerStyle=viewerStyle)

## ----sessionInfo, results='asis'-----------------------------------------
sessionInfo()