---
title: "trackViewer Vignette"
author: "Jianhong Ou, Lihua Julie Zhu"
date: "`r doc_date()`"
package: "`r pkg_ver('trackViewer')`"
abstract: >
  visualize mapped reads along with annotation as track layers for NGS dataset 
  such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq.
vignette: >
  %\VignetteIndexEntry{trackViewer Vignette}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
output:
  BiocStyle::html_document
---

# Introduction

There are two packages available in Bioconductor for visualizing genomic data: **rtracklayer** and **Gviz**. **rtracklayer** provides an interface to genome browsers and associated annotation tracks. **Gviz** plots data and annotation information along genomic coordinates. **TrackViewer** is a light-weighted visualization tool for generating neat figures for publication. It utilizes **Gviz**, is easy to use, and has a low memory and cpu consumption.

```{r 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="-")
```
```{r 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)
```

**TrackViewer**  not only has the functionalities to  plot the figures generated by **Gviz**, as shown in Figure above, but also provides additional plotting styles as shown in Figure below. The mimimalist design requires minimum input from users while retaining the flexibility to change output style easily. 


```{r 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)
```
```{r 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)
```


It requires huge memory space to handle big wig files. To solve this problem, **trackViewer** rewrote the import function to import whole file first and parse it later when plot. **trackViewer** provides higher import speed (21 min vs. over 180 min) and acceptable memory cost (5.32G vs. over 10G) for a half giga wig file (GSM917672) comparing to **Gviz**. 

# Steps of using \Biocpkg{trackViewer}
## step1 import data
Function **importScore** is used to import BED, WIG, bedGraph or BigWig files. 
Function **importBam** is employed to import bam file. Here is the example.

```{r 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) <- "+"
```

Function **coverageGR** could be used to calculate coverage after importing if
needed.

```{r 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)=="-"]
```

## step2 build gene model
The gene model can be built for a given genomic range using **geneModelFromTxdb**
function which uses **TranscriptDb** object as input.

```{r geneModel}
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
trs <- geneModelFromTxdb(TxDb.Hsapiens.UCSC.hg19.knownGene,
                         "chr11", 122929275, 122930122, "-")
```

## step3 view the tracks
Use **viewTracks** function to plot data and annotation information along genomic coordinates.
**addGuideLine** or **addArrowMark** can be used to highlight the peaks.
    
```{r 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)
```


# Adjust the styles
## adjust x axis or x-scale
In most cases, researchers are interested in the relative position of peaks in the gene. 
Sometimes, margin needs to be adjusted to be able to show the entire  gene model. 
Figure below shows how to add an x-scale and 
remove x-axis using **addGuideLine** Function . 

```{r optSty}
optSty <- optimizeStyle(trackList(repA, fox2, trs))
trackList <- optSty$tracks
viewerStyle <- optSty$style
```
```{r 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)
```


## adjust y axis
y-axis can be put to right side of the track by setting main slot to FALSE in y-axis slot 
of each track.
```{r 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)
```

## adjust y label
Y label style can be changed by setting the ylabgp slot in style of each track.
```{r 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)
```

Y label can be also put to top or bottom of each track.
```{r 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)
```

For each transcript, the transcript name can be put to upstream or downstream of
the transcript.

```{r 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)
```


## adjust track color
The track color can be changed by setting the color slot in style of each track.
The first color is for dat slot of 
**track** and seconde color is for dat2 slot.
```{r 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)
```

## adjust track height
The track height can be changed by setting the height slot in style of each 
track. However, the total height for all 
the tracks should be 1.
```{r 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)
```

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

```{r 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)
```

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

```{r 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)
```

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

```{r 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)
```

## optimize with theme

We support two themes now: bw and col.
```{r 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)
```

```{r 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)
```

# Operators
If there are two tracks and we want to draw the two track by adding or substract 
one from another, we can try operators.

```{r 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="+")
```

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

Or try **GRoperator** before view tracks.

```{r 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)
```

# Session Info
```{r sessionInfo, results='asis'}
sessionInfo()
```