## ----init, echo=FALSE, results='hide'-----------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
## comment = "#>",
error = FALSE,
warning = FALSE,
message = FALSE,
crop = NULL # fix vignette rendering based on yihui/knitr#1796 , added also error=FALSE to include_graphics
)
## stopifnot(requireNamespace("htmltools"))
## htmltools::tagList(rmarkdown::html_dependency_font_awesome())
## check the output type
out_type <- knitr::opts_knit$get("rmarkdown.pandoc.to")
## add styling
if (out_type == "html") {
BiocStyle::markdown()
## BiocStyle::markdown(css.files = c('custom.css'))
} else if (out_type == "latex") {
BiocStyle::latex()
}
## ----init2, echo=FALSE, results='hide'----------------------------------------
library(knitr)
source(system.file("scripts/documentation.R", package="Gviz"))
xtabDetails <- details
addParTable <- function(xtabDetails, class, skip=c("showTitle", "size", "background.title"), add=NULL, out_type="html") {
Parameters <- data.frame("Display Parameter"=names(xtabDetails[[class]]),
"Description"=xtabDetails[[class]], check.names=FALSE)
if(!is.null(add)) {
Parameters <- cbind(Parameters, add)
}
Parameters <- Parameters[order(Parameters[,1]),]
sel <- !Parameters[,1] %in% skip
Parameters <- Parameters[sel,]
Parameters[,2] <- gsub("\\\\\\code\\{(.*?)\\}", "`\\1`", Parameters[,2])
Parameters[,2] <- gsub("\\\\\\link[sS]4[Cc]lass\\{(.*?)\\}", "\\1", Parameters[,2])
Parameters[,2] <- gsub("\\\\\\link\\{(.*?)\\}", "\\1", Parameters[,2])
rownames(Parameters) <- NULL
if (out_type == "html") {
out <- kable(Parameters) # %>% kable_styling(full_width = FALSE)
} else if (out_type == "latex") {
out <- kable(Parameters, format="latex", booktabs=TRUE, longtable=TRUE) # %>% kable_styling(full_width = FALSE, latex_options = "hold_position")
}
print(out)
return(invisible())
}
hasUcscConnection <- !is(try(rtracklayer::browserSession(), silent=TRUE), "try-error")
oto <- options(timeout=5)
hasBiomartConnection <- (!is(try(download.file("http://www.biomart.org", tempfile(), quiet=TRUE)), "try-error") &&
!is(try(biomaRt::listMarts(), silent=TRUE), "try-error"))
## hasBiomartConnection <- FALSE
options(timeout=oto)
## ## Uncommenting this helps when the UCSC server has a hickup but still lets you connect:
## hasUcscConnection <- !is(try(rtracklayer::browserSession(), silent=TRUE), "try-error") && !is(try(IdeogramTrack(genome="hg19", chromosome=7), silent=TRUE), "try-error")
## ----loadPackage, cache=FALSE-------------------------------------------------
library(Gviz)
## ----AnnotationTrack----------------------------------------------------------
library(GenomicRanges)
data(cpgIslands)
class(cpgIslands)
chr <- as.character(unique(seqnames(cpgIslands)))
gen <- genome(cpgIslands)
atrack <- AnnotationTrack(cpgIslands, name="CpG")
## ----plotAnnotationTrack, fig.width=7.5, fig.height=0.5-----------------------
plotTracks(atrack)
## ----GenomeAxisTrack----------------------------------------------------------
gtrack <- GenomeAxisTrack()
## ----plotGenomeAxisTrack, fig.width=7.5, fig.height=1.1-----------------------
plotTracks(list(gtrack, atrack))
## ----showIdeogramTrack, eval=FALSE--------------------------------------------
# itrack <- IdeogramTrack(genome=gen, chromosome=chr)
## ----doIdeogramTrack, echo=FALSE, results='hide'------------------------------
if(hasUcscConnection){
itrack <- IdeogramTrack(genome=gen, chromosome=chr)
}else{
data(itrack)
}
## ----plotIdeogramTrack, fig.width=7.5, fig.height=1.5-------------------------
plotTracks(list(itrack, gtrack, atrack))
## ----GeneRegionTrack, fig.width=7.5, fig.height=3-----------------------------
data(geneModels)
grtrack <- GeneRegionTrack(geneModels, genome=gen, chromosome=chr, name="Gene Model")
plotTracks(list(itrack, gtrack, atrack, grtrack))
## ----zooming, fig.width=7.5, fig.height=2.2-----------------------------------
plotTracks(list(itrack, gtrack, atrack, grtrack), from=26700000, to=26750000)
## ----zooming2, fig.width=7.5, fig.height=3------------------------------------
plotTracks(list(itrack, gtrack, atrack, grtrack), extend.left=0.5, extend.right=1000000)
## ----zooming3, fig.width=7.5, fig.height=3------------------------------------
plotTracks(list(itrack, gtrack, atrack, grtrack), extend.left=0.5, extend.right=1000000, col=NULL)
## ----zooming4, fig.width=7.5, fig.height=3.1----------------------------------
library(BSgenome.Hsapiens.UCSC.hg19)
strack <- SequenceTrack(Hsapiens, chromosome=chr)
plotTracks(list(itrack, gtrack, atrack, grtrack, strack), from=26591822, to=26591852, cex=0.8)
## ----DataTrack, fig.width=7.5, fig.height=4-----------------------------------
set.seed(255)
lim <- c(26700000, 26750000)
coords <- sort(c(lim[1], sample(seq(from=lim[1], to=lim[2]), 99), lim[2]))
dat <- runif(100, min=-10, max=10)
dtrack <- DataTrack(data=dat, start=coords[-length(coords)], end=coords[-1], chromosome=chr,
genome=gen, name="Uniform")
plotTracks(list(itrack, gtrack, atrack, grtrack, dtrack), from=lim[1], to=lim[2])
## ----DataTrackHist, fig.width=7.5, fig.height=4-------------------------------
plotTracks(list(itrack, gtrack, atrack, grtrack, dtrack), from=lim[1], to=lim[2], type="histogram")
## ----displayPars1f, fig.width=7.5, fig.height=3-------------------------------
grtrack <- GeneRegionTrack(geneModels, genome=gen, chromosome=chr, name="Gene Model", transcriptAnnotation="symbol", background.title="brown")
head(displayPars(grtrack))
displayPars(grtrack) <- list(background.panel="#FFFEDB", col=NULL)
head(displayPars(grtrack))
plotTracks(list(itrack, gtrack, atrack, grtrack))
## ----displayPars2f, fig.width=7.5, fig.height=3-------------------------------
plotTracks(list(itrack, gtrack, atrack, grtrack), background.panel="#FFFEDB", background.title="darkblue")
## ----displayPars3-------------------------------------------------------------
dp <- availableDisplayPars(grtrack)
tail(dp)
## ----displayPars4, fig.width=7.5, fig.height=1.5------------------------------
getOption("Gviz.scheme")
scheme <- getScheme()
scheme$GeneRegionTrack$fill <- "salmon"
scheme$GeneRegionTrack$col <- NULL
scheme$GeneRegionTrack$transcriptAnnotation <- "transcript"
addScheme(scheme, "myScheme")
options(Gviz.scheme="myScheme")
grtrack <- GeneRegionTrack(geneModels, genome=gen, chromosome=chr, name="Gene Model")
plotTracks(grtrack)
options(Gviz.scheme="default")
grtrack <- GeneRegionTrack(geneModels, genome=gen, chromosome=chr, name="Gene Model",
transcriptAnnotation="symbol")
## ----schemes, eval=FALSE------------------------------------------------------
# .GvizSchemes <- list(myScheme=list(GeneRegionTrack=list(fill="salmon", col=NULL, transcriptAnnotation="transcript")))
## ----plottingdirections, fig.width=7.5, fig.height=3--------------------------
plotTracks(list(itrack, gtrack, atrack, grtrack), reverseStrand=TRUE)
## ----GenomeAxisTrackClass1, fig.width=7.5, fig.height=0.5---------------------
axisTrack <- GenomeAxisTrack()
plotTracks(axisTrack, from=1e6, to=9e6)
## ----GenomeAxisTrackClass2, fig.width=7.5, fig.height=0.5---------------------
axisTrack <- GenomeAxisTrack(range=IRanges(start=c(2e6, 4e6), end=c(3e6, 7e6),
names=rep("N-stretch", 2)))
plotTracks(axisTrack, from=1e6, to=9e6)
## ----GenomeAxisTrackClass2a, fig.width=7.5, fig.height=0.5--------------------
plotTracks(axisTrack, from=1e6, to=9e6, showId=TRUE)
## ----GenomeAxisTrackClass3, fig.width=7.5, fig.height=0.5---------------------
plotTracks(axisTrack, from=1e6, to=9e6, add53=TRUE, add35=TRUE)
## ----GenomeAxisTrackClass4, fig.width=7.5, fig.height=0.5---------------------
plotTracks(axisTrack, from=1e6, to=9e6, add53=TRUE, add35=TRUE, littleTicks=TRUE)
## ----GenomeAxisTrackClass5, fig.width=7.5, fig.height=0.5---------------------
plotTracks(axisTrack, from=1e6, to=9e6, exponent=4)
## ----GenomeAxisTrackClass6, fig.width=7.5, fig.height=0.5---------------------
plotTracks(axisTrack, from=1e6, to=9e6, labelPos="below")
## ----GenomeAxisTrackClass7, fig.width=7.5, fig.height=0.5---------------------
plotTracks(axisTrack, from=1e6, to=9e6, scale=0.5)
## ----GenomeAxisTrackClass8, fig.width=7.5, fig.height=0.5---------------------
plotTracks(axisTrack, from=1e6, to=9e6, scale=0.5, labelPos="below")
## ----GenomeAxisTrackClassTable, echo=FALSE, results='asis'--------------------
addParTable(xtabDetails,"GenomeAxisTrack", out_type = out_type)
## ----IdeogramTrackClass1Show, eval=FALSE--------------------------------------
# ideoTrack <- IdeogramTrack(genome="hg19", chromosome="chrX")
# plotTracks(ideoTrack, from=85e6, to=129e6)
## ----IdeogramTrackClass1Do, fig.width=7.5, fig.height=0.5, echo=FALSE, results='hide'----
if(hasUcscConnection){
ideoTrack <- IdeogramTrack(genome="hg19", chromosome="chrX")
}else{
data(itrack)
}
plotTracks(ideoTrack, from=85e6, to=129e6)
## ----IdeogramTrackClass2, fig.width=7.5, fig.height=0.5-----------------------
plotTracks(ideoTrack, from=85e6, to=129e6, showId=FALSE)
## ----IdeogramTrackClass3, fig.width=7.5, fig.height=0.5-----------------------
plotTracks(ideoTrack, from=85e6, to=129e6, showId=FALSE, showBandId=TRUE, cex.bands=0.5)
## ----IdeogramTrackClassTable, echo=FALSE, results='asis'----------------------
addParTable(xtabDetails,"IdeogramTrack", out_type = out_type)
## ----DataClass1, fig.width=7.5, fig.height=1.5--------------------------------
data(twoGroups)
dTrack <- DataTrack(twoGroups, name="uniform")
plotTracks(dTrack)
## ----types, echo=FALSE, results='asis'----------------------------------------
types <- data.frame(Value=c("p", "l", "b", "a", "s", "S", "g", "r", "h", "confint", "smooth", "histogram", "mountain", "polygon", "boxplot", "gradient", "heatmap", "horizon"),
Type=c("dot plot", "lines plot", "dot and lines plot", "lines plot of average (i.e., mean) values", "stair steps (horizontal first)",
"stair steps (vertical first)", "add grid lines", "add linear regression line", "histogram lines", "confidence intervals for average values", "add loess curve",
"histogram (bar width equal to range with)", "'mountain-type' plot relative to a baseline",
"'polygon-type' plot relative to a baseline", "box and whisker plot",
"false color image of the summarized values", "false color image of the individual values",
"Horizon plot indicating magnitude and direction of a change relative to a baseline"))
if (out_type == "html") {
kable(types) # %>% kable_styling(full_width = FALSE)
} else if (out_type == "latex") {
kable(types, "latex", booktabs=TRUE, longtable=TRUE) # %>% kable_styling(full_width = FALSE, latex_options = "hold_position")
}
## ----typePlots, fig.width=7.5, fig.height=8.5, echo=FALSE, results='hide'-----
pushViewport(viewport(layout=grid.layout(nrow=9, ncol=2)))
i <- 1
for(t in types$Value)
{
pushViewport(viewport(layout.pos.col=((i-1)%%2)+1, layout.pos.row=((i-1)%/%2)+1))
if(t != "horizon"){
names(dTrack) <- t
plotTracks(dTrack, type=t, add=TRUE, cex.title=0.8, margin=0.5)
}else{
data(dtHoriz)
names(dtHoriz) <- "horizon *"
plotTracks(dtHoriz[8,], type="horizon", add=TRUE, cex.title=0.8, margin=0.5, showAxis=FALSE, horizon.origin=0.7)
}
i <- i+1
popViewport(1)
}
popViewport(1)
names(dTrack) <- "uniform"
## ----mutitype, results='hide', fig.width=7.5, fig.height=1.5------------------
plotTracks(dTrack, type=c("boxplot", "a", "g"))
## ----sampNames, fig.width=7.5, fig.height=1.5---------------------------------
colnames(mcols(twoGroups))
plotTracks(dTrack, type=c("heatmap"), showSampleNames=TRUE, cex.sampleNames=0.6)
## ----grouping, results='hide', fig.width=7.5, fig.height=1.5------------------
plotTracks(dTrack, groups=rep(c("control", "treated"), each=3), type=c("a", "p", "confint"))
## ----typeGroupedPlots, fig.width=7.5, fig.height=6, echo=FALSE, results='hide'----
pushViewport(viewport(layout=grid.layout(nrow=9, ncol=1)))
i <- 1
for(t in c("a", "s", "confint", "smooth", "histogram", "boxplot", "heatmap", "horizon"))
{
pushViewport(viewport(layout.pos.col=((i-1)%%1)+1, layout.pos.row=((i-1)%/%1)+1))
if(t != "horizon"){
names(dTrack) <- t
plotTracks(dTrack, type=t, add=TRUE, cex.title=0.8, groups=rep(1:2, each=3), margin=0.5)
}else{
plotTracks(dtHoriz[c(1,8),], type="horizon", add=TRUE, cex.title=0.8, margin=0.5, showAxis=FALSE, horizon.origin=0.3,
groups=1:2)
}
i <- i+1
popViewport(1)
}
pushViewport(viewport(layout.pos.col=((i-1)%%1)+1, layout.pos.row=((i-1)%/%1)+1))
names(dTrack) <- "hor. hist."
plotTracks(dTrack, type="histogram", stackedBars=FALSE, add=TRUE, cex.title=0.8, groups=rep(1:2, each=3), margin=0.5)
popViewport(2)
names(dTrack) <- "uniform"
## ----groupingLegend, results='hide', fig.width=7.5, fig.height=1.5------------
plotTracks(dTrack, groups=rep(c("control", "treated"), each=3), type=c("a", "p"), legend=TRUE)
## ----horizLegend, results='hide', fig.width=7.5, fig.height=1.5---------------
data(dtHoriz)
dtHoriz <- dtHoriz[1:6,]
plotTracks(dtHoriz, type="horiz", groups=rownames(values(dtHoriz)),
showSampleNames=TRUE, cex.sampleNames = 0.6, separator=1)
## ----filedt1, fig.width=7.5, fig.height=1-------------------------------------
bgFile <- system.file("extdata/test.bedGraph", package="Gviz")
dTrack2 <- DataTrack(range=bgFile, genome="hg19", type="l", chromosome="chr19", name="bedGraph")
class(dTrack2)
plotTracks(dTrack2)
## ----filedt2------------------------------------------------------------------
library(rtracklayer)
dTrack3 <- DataTrack(range=bgFile, genome="hg19", type="l", chromosome="chr19", name="bedGraph",
importFunction=function(file) import(con=file))
identical(dTrack2, dTrack3)
## ----filedt3, fig.width=7.5, fig.height=1-------------------------------------
bamFile <- system.file("extdata/test.bam", package="Gviz")
dTrack4 <- DataTrack(range=bamFile, genome="hg19", type="l", name="Coverage", window=-1, chromosome="chr1")
class(dTrack4)
dTrack4
plotTracks(dTrack4, from=189990000, to=190000000)
## ----filedt4, fig.width=7.5, fig.height=1-------------------------------------
plotTracks(dTrack4, chromosome="chr1", from=189891483, to=190087517)
## ----filedt5------------------------------------------------------------------
myImportFun <- function(file, selection){
## do something here
}
DataTrack(range=bamFile, genome="hg19", type="l", name="Coverage", window=-1, chromosome="chr1",
importFunction=myImportFun, stream=TRUE)
## ----biggerdata, results='hide', fig.width=7.5, fig.height=1.5----------------
dat <- sin(seq(pi, 10*pi, len=500))
dTrack.big <- DataTrack(start=seq(1,100000, len=500), width=15, chromosome="chrX",
genome="hg19", name="sinus",
data=sin(seq(pi, 5*pi, len=500))*runif(500, 0.5, 1.5))
plotTracks(dTrack.big, type="hist")
## ----aggregation, results='hide', fig.width=7.5, fig.height=1.5---------------
plotTracks(dTrack.big, type="hist", window=50)
## ----aggregation2, results='hide', fig.width=7.5, fig.height=1.5--------------
plotTracks(dTrack.big, type="hist", window=-1, windowSize=2500)
## ----transformation, results='hide', fig.width=7.5, fig.height=1.5------------
plotTracks(dTrack.big, type="l", transformation=function(x){x[x<0] <- 0; x})
## ----groupingAv1, results='hide', fig.width=7.5, fig.height=1.5---------------
plotTracks(dTrack, groups=rep(c("control", "treated"), each=3), type=c("b"), aggregateGroups=TRUE)
## ----groupingAv2, results='hide', fig.width=7.5, fig.height=1.5---------------
plotTracks(dTrack, groups=rep(c("control", "treated"), each=3), type=c("b"), aggregateGroups=TRUE, aggregation="max")
## ----DataTrackClassTable, echo=FALSE, results='asis'--------------------------
addParTable(xtabDetails,"DataTrack", out_type = out_type)
## ----anntrack1, results='hide', fig.width=7.5, fig.height=0.5-----------------
aTrack <- AnnotationTrack(start=c(10, 40, 120), width=15, chromosome="chrX",
strand=c("+", "*", "-"),
id=c("Huey", "Dewey", "Louie"), genome="hg19", name="foo")
plotTracks(aTrack)
## ----anntrack2, results='hide', fig.width=7.5, fig.height=0.5-----------------
plotTracks(aTrack, shape="box", featureAnnotation="id")
## ----anntrack3, results='hide', fig.width=7.5, fig.height=0.5-----------------
plotTracks(aTrack, shape="ellipse", featureAnnotation="id", fontcolor.feature="darkblue")
## ----anntrack4f, results='hide', fig.width=7.5, fig.height=0.5----------------
aTrack.groups <- AnnotationTrack(start=c(50, 180, 260, 460, 860, 1240), width=c(15,20,40,100,200, 20),
chromosome="chrX",
strand=rep(c("+", "*", "-"), c(1,3,2)),
group=rep(c("Huey", "Dewey", "Louie"), c(1,3,2)),
genome="hg19", name="foo")
plotTracks(aTrack.groups, groupAnnotation="group")
## ----anntrack4af, results='hide', fig.width=7.5, fig.height=0.5---------------
plotTracks(aTrack.groups, groupAnnotation="group", just.group="right")
## ----anntrack4bf, results='hide', fig.width=7.5, fig.height=0.5---------------
plotTracks(aTrack.groups, groupAnnotation="group", just.group="above")
## ----stacking1, results='hide', fig.width=7.5, fig.height=0.5-----------------
aTrack.stacked <- AnnotationTrack(start=c(50, 180, 260, 800, 600, 1240), width=c(15,20,40,100,500, 20),
chromosome="chrX",
strand="*",
group=rep(c("Huey", "Dewey", "Louie"), c(1,3,2)),
genome="hg19", name="foo")
plotTracks(aTrack.stacked, groupAnnotation="group")
## ----stacking2, results='hide', fig.width=7.5, fig.height=0.5-----------------
plotTracks(aTrack.stacked, stacking="dense")
## ----features-----------------------------------------------------------------
feature(aTrack.stacked)
feature(aTrack.stacked)<- c("foo", "bar", "bar", "bar", "no", "no")
## ----featuresIdPlot, results='hide', fig.width=7.5, fig.height=0.5------------
plotTracks(aTrack.stacked, featureAnnotation="feature", groupAnnotation="feature", fontcolor.feature=1, cex.feature=0.7)
## ----featuresPlotf, results='hide', fig.width=7.5, fig.height=0.5-------------
plotTracks(aTrack.stacked, groupAnnotation="group", foo="darkred", bar="darkgreen")
## ----overplotting, results='hide', fig.width=7.5, fig.height=0.75-------------
data("denseAnnTrack")
plotTracks(denseAnnTrack, showOverplotting=TRUE)
## ----collapse1f, results='hide', fig.width=7.5, fig.height=0.85---------------
data(collapseTrack)
plotTracks(ctrack)
## ----collapse2f, results='hide', fig.width=7.5, fig.height=0.85---------------
plotTracks(ctrack, min.width=1)
## ----collapse3f, results='hide', fig.width=7.5, fig.height=0.85---------------
plotTracks(ctrack, min.width=1, collapse=TRUE)
## ----collapse4f, results='hide', fig.width=7.5, fig.height=0.85---------------
plotTracks(ctrack, min.width=3, min.distance=5, collapse=TRUE)
## ----collapse5f, results='hide', fig.width=7.5, fig.height=0.65---------------
plotTracks(ctrack, min.width=3, min.distance=5, collapse=TRUE,
mergeGroups=TRUE, extend.left=0.1)
## ----fileat1, fig.width=7.5, fig.height=1-------------------------------------
aTrack2 <- AnnotationTrack(range=bamFile, genome="hg19", name="Reads", chromosome="chr1")
class(aTrack2)
aTrack2
plotTracks(aTrack2, from=189995000, to=190000000)
## ----fileat2, fig.width=7.5, fig.height=1-------------------------------------
aTrack3 <- AnnotationTrack(range=bamFile, genome="hg19", name="Reads", chromosome="chr1", group="id")
aTrack3
plotTracks(aTrack3, from=189995000, to=190000000)
## ----fileat3------------------------------------------------------------------
availableDefaultMapping(bamFile, "AnnotationTrack")
## ----fileat4, fig.width=7.5, fig.height=2-------------------------------------
plotTracks(list(dTrack4, aTrack2), from=189990000, to=190000000)
## ----AnnotationTrackClassTable, echo=FALSE, results='asis'--------------------
addParTable(xtabDetails,"AnnotationTrack", out_type = out_type)
## ----generegtrackf, results='hide', fig.width=7.5, fig.height=1.5-------------
data(geneModels)
grtrack <- GeneRegionTrack(geneModels, genome=gen, chromosome=chr, name="foo")
head(gene(grtrack))
head(transcript(grtrack))
head(exon(grtrack))
head(symbol(grtrack))
plotTracks(grtrack)
## ----generegtrack2af, results='hide', fig.width=7.5, fig.height=2.5-----------
plotTracks(grtrack, transcriptAnnotation="symbol")
## ----generegtrack2bf, results='hide', fig.width=7.5, fig.height=2.5-----------
plotTracks(grtrack, transcriptAnnotation="transcript")
## ----generegtrack2cf, results='hide', fig.width=7.5, fig.height=1-------------
plotTracks(grtrack, exonAnnotation="exon", extend.left=-0.8, fontcolor.exon=1)
## ----generegtrack3f, results='hide', fig.width=7.5, fig.height=1--------------
plotTracks(grtrack, collapseTranscripts=TRUE, shape="arrow", transcriptAnnotation="symbol")
## ----generegtrack3g, results='hide', fig.width=7.5, fig.height=1--------------
plotTracks(grtrack, collapseTranscripts="longest", shape="arrow", transcriptAnnotation="symbol")
## ----generegtrack3h, results='hide', fig.width=7.5, fig.height=1--------------
plotTracks(grtrack, collapseTranscripts="meta", shape="arrow", transcriptAnnotation="symbol")
## ----tdb2grt1-----------------------------------------------------------------
library(GenomicFeatures)
samplefile <- system.file("extdata", "hg19_knownGene_sample.sqlite", package="GenomicFeatures")
txdb <- loadDb(samplefile)
GeneRegionTrack(txdb)
## ----tdb2grt2-----------------------------------------------------------------
txTr <- GeneRegionTrack(txdb, chromosome="chr6", start=35000000, end=40000000)
## ----generegtrack4f, results='hide', fig.width=7.5, fig.height=0.35-----------
feature(txTr)
plotTracks(txTr)
## ----GeneRegionTrackClassTable, echo=FALSE, results='asis'--------------------
addParTable(xtabDetails,"GeneRegionTrack", out_type = out_type)
## ----BiomartGeneRegionTrackShow, eval=FALSE-----------------------------------
# library(biomaRt)
# bm <- useMart(host="grch37.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
# biomTrack <- BiomartGeneRegionTrack(genome="hg19", chromosome=chr, start=20e6, end=21e6,
# name="ENSEMBL", biomart=bm)
# plotTracks(biomTrack)
## ----BiomartGeneRegionTrackDo, echo=FALSE, results='hide', fig.width=7.5, fig.height=1.25----
library(biomaRt)
if(hasBiomartConnection){
bm <- useMart(host="grch37.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
biomTrack <- BiomartGeneRegionTrack(genome="hg19", chromosome=chr, start=20e6, end=21e6,
name="ENSEMBL", biomart=bm)
}else{
data("biomTrack")
}
plotTracks(biomTrack)
## ----BiomartGeneRegionTrackCol, fig.width=7.5, fig.height=1.25----------------
plotTracks(biomTrack, col.line=NULL, col=NULL)
## ----BiomartGeneRegionTrackHeight, fig.width=7.5, fig.height=1.25-------------
plotTracks(biomTrack, col.line=NULL, col=NULL, stackHeight=0.3)
## ----BiomartGeneRegionTrackFilterShow, eval=FALSE-----------------------------
# bm <- useMart(host="grch37.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
# biomTrack <- BiomartGeneRegionTrack(genome="hg19", chromosome=chr, start=20e6, end=21e6,
# name="ENSEMBL", filter=list(with_refseq_mrna=TRUE), biomart=bm)
# plotTracks(biomTrack, col.line=NULL, col=NULL, stackHeight=0.3)
## ----BiomartGeneRegionTrackFilterDo, fig.width=7.5, fig.height=1.25, echo=FALSE, results='hide'----
if(hasBiomartConnection){
bm <- useMart(host="grch37.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
biomTrack <- BiomartGeneRegionTrack(genome="hg19", chromosome=chr, start=20e6, end=21e6,
name="ENSEMBL", filter=list(with_refseq_mrna=TRUE), biomart=bm)
plotTracks(biomTrack, col.line=NULL, col=NULL, stackHeight=0.3)
}else{
biomTrack@filter <- list(with_refseq_mrna=TRUE)
plotTracks(biomTrack, col.line=NULL, col=NULL, stackHeight=0.3)
biomTrack@filter <- list()
}
## ----BiomartGeneRegionTrackSymbolShow, eval=FALSE-----------------------------
# bm <- useMart(host="grch37.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
# biomTrack <- BiomartGeneRegionTrack(genome="hg19", name="ENSEMBL", symbol="ABCB5", biomart=bm)
# plotTracks(biomTrack, transcriptAnnotation="symbol")
## ----BiomartGeneRegionTrackSymbolDo, fig.width=7.5, fig.height=1.25, echo=FALSE, results='hide'----
if(hasBiomartConnection){
bm <- useMart(host="grch37.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
biomTrack <- BiomartGeneRegionTrack(genome="hg19", name="ENSEMBL", symbol="ABCB5", biomart=bm)
}else{
ranges(biomTrack) <- ranges(biomTrack)[symbol(biomTrack) == "ABCB5"]
}
plotTracks(biomTrack, transcriptAnnotation="symbol")
## ----BiomartGeneRegionTrackCustom, fig.width=7.5, fig.height=1.25, eval=FALSE, echo=F----
# library(biomaRt)
# bm <- useMart(host="dec2012.archive.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL",
# dataset="hsapiens_gene_ensembl")
# fm <- Gviz:::.getBMFeatureMap()
# fm[["symbol"]] <- "external_gene_id"
# biomTrack <- BiomartGeneRegionTrack(genome="hg19", chromosome="chr7", start=20e6, end=21e6,name="ENSEMBL",
# featureMap=fm, biomart=bm)
# plotTracks(biomTrack, col.line=NULL, col=NULL, stackHeight=0.3)
## ----BiomartGeneRegionTrackClassTable, echo=FALSE, results='asis'-------------
addInfo <- t(data.frame(displayPars(biomTrack, names(details[["BiomartGeneRegionTrack"]]))))
colnames(addInfo) <- "Color"
addParTable(xtabDetails,"BiomartGeneRegionTrack", add=addInfo, out_type = out_type)
## ----DetailsAnnotationTrack1--------------------------------------------------
library(GenomicRanges)
probes <- GRanges(seqnames="chr7", ranges=IRanges(start=c(2000000, 2070000, 2100000, 2160000), end=c(2050000, 2130000, 2150000, 2170000)),
strand=c("-", "+", "-", "-"))
## ----DetailsAnnotationTrack2--------------------------------------------------
methylation <- matrix(c(rgamma(400, 1)), ncol=100, dimnames=list(paste("probe", 1:4, sep=""), NULL))
methylation[,51:100] <- methylation[,51:100] + 0:3
sgroups <- rep(c("grp1","grp2"), each=50)
## ----DetailsAnnotationTrack3--------------------------------------------------
library(lattice)
details <- function(identifier, ...) {
d <- data.frame(signal=methylation[identifier,], group=sgroups)
print(densityplot(~signal, group=group, data=d, main=list(label=identifier, cex=0.7),
scales=list(draw=FALSE, x=list(draw=TRUE)), ylab="", xlab="",
), newpage=FALSE, prefix="plot")
}
## ----DetailsAnnotationTrack4, results='hide', fig.width=7.5, fig.height=5-----
deTrack <- AnnotationTrack(range=probes, genome="hg19", chromosome=7, id=rownames(methylation),
name="probe details", stacking="squish",
fun=details)
plotTracks(deTrack)
## ----DetailsAnnotationTrack5--------------------------------------------------
selFun <- function(identifier, start, end, track, GdObject, ...){
gcount <- table(group(GdObject))
## This computes the width of 2 pixels in genomic coordinates
pxRange <- Gviz:::.pxResolution(min.width=20, coord="x")
return((end-start)<pxRange && gcount[identifier]==1)
}
## ----DetailsAnnotationTrack6--------------------------------------------------
detFun <- function(identifier, GdObject.original, ...){
plotTracks(list(GenomeAxisTrack(scale=0.3, size=0.2, cex=0.7), GdObject.original[group(GdObject.original)==identifier]),
add=TRUE, showTitle=FALSE)
}
## ----DetailsAnnotationTrack7f, results='hide', fig.width=7.5, fig.height=2----
data(geneDetails)
deTrack2 <- AnnotationTrack(geneDetails, fun=detFun, selectFun=selFun,
groupDetails=TRUE, details.size=0.5, detailsConnector.cex=0.5, detailsConnector.lty="dotted",
shape=c("smallArrow", "arrow"), groupAnnotation="group")
plotTracks(deTrack2, extend.left=90000)
## ----DetailsAnnotationTrack8, results='hide', fig.width=7.5, fig.height=3-----
plotTracks(deTrack, details.size=0.75, detailsConnector.pch=NA, detailsConnector.col="darkred",
detailsBorder.fill="#FFE3BF", detailsBorder.col="darkred", shape="box", detailsConnector.lty="dotted")
## ----DetailsAnnotationTrackClassTableSec, echo=FALSE, results='asis'----------
addParTable(xtabDetails,"DetailsAnnotationTrack", out_type = out_type)
## ----SequenceTrack1-----------------------------------------------------------
library(BSgenome.Hsapiens.UCSC.hg19)
sTrack <- SequenceTrack(Hsapiens)
sTrack
## ----SequenceTrack2, results='hide', fig.width=7.5, fig.height=0.5------------
plotTracks(sTrack, chromosome=1, from=20000, to=20050)
## ----SequenceTrack3, results='hide', fig.width=7.5, fig.height=0.5------------
fcol <- c(A="darkgray", C="darkgray", T="darkgray", G="darkgray")
plotTracks(sTrack, chromosome=1, from=20000, to=20050, fontcolor=fcol)
## ----SequenceTrack4, results='hide', fig.width=7.5, fig.height=0.5------------
plotTracks(sTrack, chromosome=1, from=20000, to=20050, add53=TRUE)
## ----SequenceTrack5, results='hide', fig.width=7.5, fig.height=0.3------------
plotTracks(sTrack, chromosome=1, from=20000, to=20050, add53=TRUE, complement=TRUE)
## ----SequenceTrack6, results='hide', fig.width=7.5, fig.height=0.3------------
plotTracks(sTrack, chromosome=1, from=20000, to=20100)
## ----SequenceTrack7, results='hide', fig.width=7.5, fig.height=0.3------------
plotTracks(sTrack, chromosome=1, from=20000, to=201000)
## ----SequenceTrack8, results='hide', fig.width=7.5, fig.height=0.3------------
plotTracks(sTrack, chromosome=1, from=20000, to=20100, cex=0.5)
## ----SequenceTrackClassTableSec, echo=FALSE, results='asis'-------------------
addParTable(xtabDetails,"SequenceTrack", out_type = out_type)
## ----alignmentstrack_1_do, echo=FALSE, results='hide'-------------------------
afrom <- 2960000
ato <- 3160000
alTrack <- AlignmentsTrack(system.file(package="Gviz", "extdata", "gapped.bam"), isPaired=TRUE)
data(alTrackGenes)
## ----alignmentstrack_1_show, eval=FALSE---------------------------------------
# afrom <- 2960000
# ato <- 3160000
# alTrack <- AlignmentsTrack(system.file(package="Gviz", "extdata", "gapped.bam"), isPaired=TRUE)
# bmt <- BiomartGeneRegionTrack(genome="hg19", chromosome="chr12", start=afrom, end=ato,
# filter=list(with_refseq_mrna=TRUE), stacking="dense")
## ----alignmentstrack_2, results='hide', fig.width=7.5, fig.height=5-----------
plotTracks(c(bmt, alTrack), from=afrom, to=ato, chromosome="chr12")
## ----alignmentstrack_3, results='hide', fig.width=7.5, fig.height=5-----------
plotTracks(c(bmt, alTrack), from=afrom, to=ato, chromosome="chr12", min.height=0, coverageHeight=0.08,
minCoverageHeight=0)
## ----alignmentstrack_4, results='hide', fig.width=7.5, fig.height=2-----------
plotTracks(c(alTrack, bmt), from=afrom, to=ato, chromosome="chr12", type="coverage")
## ----alignmentstrack_5, results='hide', fig.width=7.5, fig.height=5-----------
plotTracks(c(bmt, alTrack), from=afrom+12700, to=afrom+15200, chromosome="chr12")
## ----alignmentstrack_5_1, results='hide', fig.width=7.5, fig.height=2---------
plotTracks(c(bmt, alTrack), from=afrom+12700, to=afrom+15200, chromosome="chr12",
type=c("coverage", "sashimi"))
## ----alignmentstrack_5_2, results='hide', fig.width=7.5, fig.height=2---------
introns <- GRanges("chr12", IRanges(start=c(2973662, 2973919), end=c(2973848, 2974520)))
plotTracks(c(bmt, alTrack), from=afrom+12700, to=afrom+15200, chromosome="chr12",
type=c("coverage", "sashimi"), sashimiFilter=introns)
## ----alignmentstrack_5_3, results='hide', fig.width=7.5, fig.height=2---------
plotTracks(c(bmt, alTrack), from=afrom+12700, to=afrom+15200, chromosome="chr12",
type=c("coverage", "sashimi"), sashimiFilter=introns, sashimiFilterTolerance=5L)
## ----alignmentstrack_6, results='hide', fig.width=7.5, fig.height=5-----------
plotTracks(c(bmt, alTrack), from=afrom+12700, to=afrom+15200, chromosome="chr12", reverseStacking=TRUE,
col.mates="purple", col.gap="orange", type="pileup")
## ----alignmentstrack_6_1, results='hide', fig.width=7.5, fig.height=5---------
alTrack <- AlignmentsTrack(system.file(package="Gviz", "extdata", "gapped.bam"), isPaired=FALSE)
plotTracks(c(bmt, alTrack), from=afrom+12700, to=afrom+15200, chromosome="chr12")
## ----alignmentstrack_7, results='hide', fig.width=7.5, fig.height=5-----------
afrom <- 44945200
ato <- 44947200
alTrack <- AlignmentsTrack(system.file(package="Gviz", "extdata", "snps.bam"), isPaired=TRUE)
plotTracks(alTrack, chromosome="chr21", from=afrom, to=ato)
## ----alignmentstrack_8, results='hide', fig.width=7.5, fig.height=5-----------
plotTracks(c(alTrack, sTrack), chromosome="chr21", from=afrom, to=ato)
## ----alignmentstrack_9, results='hide', fig.width=7.5, fig.height=5-----------
plotTracks(c(alTrack, sTrack), chromosome="chr21", from=44946590, to=44946660)
## ----alignmentstrack_10, results='hide', fig.width=7.5, fig.height=5----------
plotTracks(c(alTrack, sTrack), chromosome="chr21", from=44946590, to=44946660, cex=0.5, min.height=8)
## ----AlignmentsTrackClassTable, echo=FALSE, results='asis'--------------------
addParTable(xtabDetails,"AlignmentsTrack", out_type = out_type)
## ----UCSC1, echo=FALSE,fig.cap="A screen shot of a UCSC genome browser view around the FMR1 locus on the mouse chromosome."----
include_graphics("ucsc1.png")
## ----UCSC2, echo=FALSE, fig.cap="A screen shot of a UCSC table browser view on the UCSC Known Genes track."----
include_graphics("ucsc2.png")
## ----ucscTrack1, eval=FALSE---------------------------------------------------
# from <- 65921878
# to <- 65980988
# knownGenes <- UcscTrack(genome="mm9", chromosome="chrX", track="knownGene", from=from, to=to,
# trackType="GeneRegionTrack", rstarts="exonStarts", rends="exonEnds", gene="name",
# symbol="name", transcript="name", strand="strand", fill="#8282d2", name="UCSC Genes")
## ----ucscTrack2, eval=FALSE---------------------------------------------------
# refGenes <- UcscTrack(genome="mm9", chromosome="chrX", track="xenoRefGene", from=from, to=to,
# trackType="GeneRegionTrack", rstarts="exonStarts", rends="exonEnds", gene="name",
# symbol="name2", transcript="name", strand="strand", fill="#8282d2",
# stacking="dense", name="Other RefSeq")
#
# ensGenes <- UcscTrack(genome="mm9", chromosome="chrX", track="ensGene", from=from, to=to,
# trackType="GeneRegionTrack", rstarts="exonStarts", rends="exonEnds", gene="name",
# symbol="name2", transcript="name", strand="strand", fill="#960000",
# name="Ensembl Genes")
## ----ucscTrack3, eval=FALSE---------------------------------------------------
# cpgIslands <- UcscTrack(genome="mm9", chromosome="chrX", track="cpgIslandExt", from=from, to=to,
# trackType="AnnotationTrack", start="chromStart", end="chromEnd", id="name",
# shape="box", fill="#006400", name="CpG Islands")
#
# snpLocations <- UcscTrack(genome="mm9", chromosome="chrX", track="snp128", from=from, to=to,
# trackType="AnnotationTrack", start="chromStart", end="chromEnd", id="name",
# feature="func", strand="strand", shape="box", stacking="dense", fill="black",
# name="SNPs")
## ----ucscTrack4, eval=FALSE---------------------------------------------------
# conservation <- UcscTrack(genome="mm9", chromosome="chrX", track="Conservation", table="phyloP30wayPlacental",
# from=from, to=to, trackType="DataTrack", start="start", end="end", data="score",
# type="hist", window="auto", col.histogram="darkblue", fill.histogram="darkblue",
# ylim=c(-3.7, 4), name="Conservation")
#
# gcContent <- UcscTrack(genome="mm9", chromosome="chrX", track="GC Percent", table="gc5Base",
# from=from, to=to, trackType="DataTrack", start="start", end="end", data="score",
# type="hist", window=-1, windowSize=1500, fill.histogram="black", col.histogram="black",
# ylim=c(30, 70), name="GC Percent")
## ----ucscTrack5, eval=FALSE---------------------------------------------------
# axTrack <- GenomeAxisTrack()
# idxTrack <- IdeogramTrack(genome="mm9", chromosome="chrX")
## ----ucscTrackLoad, echo=FALSE, results='hide'--------------------------------
data(ucscItems)
## ----ucscTrack6, results='hide', fig.width=7.5, fig.height=5.5----------------
plotTracks(list(idxTrack, axTrack, knownGenes, refGenes, ensGenes, cpgIslands,
gcContent, conservation, snpLocations), from=from, to=to, showTitle=FALSE)
## ----HighlightTrack, fig.width=7.5, fig.height=4------------------------------
ht <- HighlightTrack(trackList=list(atrack, grtrack, dtrack), start=c(26705000, 26720000), width=7000, chromosome=7)
plotTracks(list(itrack, gtrack, ht), from = lim[1], to = lim[2])
## ----HighlightTrack2, fig.width=7.5, fig.height=4-----------------------------
ht1 <- HighlightTrack(trackList=list(itrack, gtrack, atrack), start=c(26705000, 26720000), width=7000, chromosome=7)
ht2 <- HighlightTrack(trackList=dtrack, start=c(26705000, 26720000), width=7000, chromosome=7)
plotTracks(list(ht1, grtrack, ht2), from=lim[1], to=lim[2])
## ----HighlightTrackClassTable, echo=FALSE, results='asis'---------------------
addParTable(xtabDetails,"HighlightTrack", out_type = out_type)
## ----OverlayTrack, fig.width=7.5, fig.height=3--------------------------------
dat <- runif(100, min=-2, max=22)
dtrack2 <- DataTrack(data=dat, start=coords[-length(coords)], end=coords[-1], chromosome=chr,
genome=gen, name="Uniform2", groups=factor("sample 2", levels=c("sample 1", "sample 2")),
legend=TRUE)
displayPars(dtrack) <- list(groups=factor("sample 1", levels=c("sample 1", "sample 2")), legend=TRUE)
ot <- OverlayTrack(trackList=list(dtrack2, dtrack))
ylims <- extendrange(range(c(values(dtrack), values(dtrack2))))
plotTracks(list(itrack, gtrack, ot), from=lim[1], to=lim[2], ylim=ylims, type=c("smooth", "p"))
## ----OverlayTrack2, fig.width=7.5, fig.height=3-------------------------------
displayPars(dtrack) <- list(alpha.title=1, alpha=0.5)
displayPars(dtrack2) <- list(alpha.title=1, alpha=0.5)
ot <- OverlayTrack(trackList=list(dtrack, dtrack2))
plotTracks(list(itrack, gtrack, ot), from=lim[1], to=lim[2], ylim=ylims, type=c("hist"), window=30)
## ----multPlot1----------------------------------------------------------------
chroms <- c("chr1", "chr2", "chr3", "chr4")
maTrack <- AnnotationTrack(range=GRanges(seqnames=chroms, ranges=IRanges(start=1, width=c(100,400,200,1000)),
strand=c("+", "+", "-", "+")), genome="mm9", chromosome="chr1", name="foo")
mdTrack <- DataTrack(range=GRanges(seqnames=rep(chroms, c(10, 40, 20, 100)),
ranges=IRanges(start=c(seq(1,100,len=10), seq(1,400,len=40), seq(1, 200, len=20),
seq(1,1000, len=100)), width=9), values=runif(170)),
data="values", chromosome="chr1", genome="mm9", name="bar")
## ----multPlot2----------------------------------------------------------------
mgTrack <- GenomeAxisTrack(scale=50, labelPos="below", exponent=3)
chromosome(itrack) <- "chr1"
## ----multPlot3, results='hide', fig.width=7.5, fig.height=4-------------------
ncols <- 2
nrows <- length(chroms)%/%ncols
grid.newpage()
pushViewport(viewport(layout=grid.layout(nrows, ncols)))
for(i in seq_along(chroms)){
pushViewport(viewport(layout.pos.col=((i-1)%%ncols)+1, layout.pos.row=(((i)-1)%/%ncols)+1))
plotTracks(list(itrack, maTrack, mdTrack, mgTrack), chromosome=chroms[i], add=TRUE)
popViewport(1)
}
## ----multPlot4, results='hide', fig.width=7.5, fig.height=4-------------------
library(lattice)
chroms <- data.frame(chromosome=chroms)
xyplot(1~chromosome|chromosome, data=chroms, panel=function(x){plotTracks(list(itrack , maTrack, mdTrack, mgTrack), chromosome=x, add=TRUE, showId=FALSE)},
scales=list(draw=FALSE), xlab=NULL, ylab=NULL)
## ----biocStruct1, echo=FALSE, results='asis'----------------------------------
dt <- data.frame(`Gviz class` = rep(c("AnnotationTrack","GeneRegionTrack","DataTrack","SequenceTrack"), c(4,5,3,2)),
`Bioconductor class`=c("data.frame","IRanges","GRanges","GRangesList",
"data.frame","IRanges","GRanges","GRangesList","TxDb",
"data.frame","IRanges","GRanges",
"DNAStringSet", "BSgenome"),
`Method`=c("Constructor","Constructor + additional arguments","Constructor or setAs method, additional data in metadata columns","Constructor or setAs method",
"Constructor","Constructor + additional arguments","Constructor or setAs method, additional data in metadata columns","Constructor or setAs method, additional data in metadata columns", "Constructor or setAs method",
"Constructor","Constructor + additional data matrix","Constructor or setAs method, numeric data in metadata columns",
"DNAStringSet & Constructor", "Constructor"),
stringsAsFactors = FALSE, check.names=FALSE)
dt[duplicated(dt[,1]),1] <- ""
if (out_type == "html") {
kable(dt) #%>% kable_styling(full_width = FALSE) %>%
#column_spec(1, bold = TRUE) %>% collapse_rows(columns = 1, valign = "top")
} else if (out_type == "latex") {
kable(dt, "latex", booktabs=TRUE, longtable=TRUE) #%>% kable_styling(full_width = FALSE, latex_options = "hold_position") %>%
#column_spec(1, bold = TRUE) %>% collapse_rows(columns = 1, valign = "top")
}
## ----biocStruct2, echo=FALSE, results='asis'----------------------------------
dt <- data.frame(`Gviz class`=rep(c("AnnotationTrack","GeneRegionTrack","DataTrack","SequenceTrack","AlignmentsTrack"), c(5, 4, 4, 2, 1)),
`File type`=c("BED","GFF","GFF2","GFF3","BAM",
"GTF","GFF","GFF2","GFF3",
"BedGraph","WIG","BigWig","BAM",
"FASTA","2Bit",
"BAM"),
`Extension`=c(".bed",".gff, .gff1, ",".gff2",".gff3",".bam",
".gtf",".gff, .gff1",".gff2",".gff3",
".bedGraph",".wig",".bigWig",".bam",
".fa, .fasta",".2bit",
".bam"),
`Streaming`=c("no","no","no","no","YES",
"no","no","no","no",
"no","no","YES","YES",
"YES","YES",
"YES"),
`Details`=c("Genomic locations from the mandatory `chrom`, `chromStart` and `chromEnd` fields, and optionally the strand from the strand field. If present, the information in the field is mapped to track item ids, and is mapped to track item feature type. All other fields are currently ignored.", "Only the following basic GFF fields are recognized: `seqname`, `start`, `end`, `strand`, (mapped to track item feature type) and `group` (to allow for track item grouping).", "Same as above, but feature grouping information may be provided either as `Group` or `Parent` attribute. Feature ids are mapped to one of the ID, Name or Alias attributes.", "Same as above, but feature grouping information has to be provided as the `Parent` attribute.", "Only start and end locations as well as the strand information for the reads are used. Read identifiers are used for track item grouping.",
"A somewhat looser format definition for `gtf` files is applied here where gene, transcript and exon identifiers and names can be parsed from the `gene_id`, `gene_name`, `transcript_id`, `transcript_name`, `exon_id`, or `exon_id attributes`", "This only supports very limited item grouping and thus complete gene models can not be properly encoded.", "In most instances this is identical to the `GTF` standard and it could make sense to rename the file accordingly.", "The gene-to-transcript and transcript-to- exon relationships are encoded in the parent and `type` attributes and the parser tries to accommodate most of the existing `GFF3` variants.",
"", "", "", "Read coverage only is extracted from the bam file.",
"Streaming only possible if an index file is found in the same directory as the original fasta file.", "",
"Always needs an index file is found in the same directory as the original `BAM` file."),
stringsAsFactors = FALSE, check.names=FALSE)
dt[duplicated(dt[,1]),1] <- ""
if (out_type == "html") {
kable(dt) #%>% kable_styling(full_width = FALSE) %>%
#column_spec(1, bold = TRUE) %>% collapse_rows(columns = 1, valign = "top")
} else if (out_type == "latex") {
kable(dt, "latex", booktabs=TRUE, longtable=TRUE) #%>% kable_styling(full_width = FALSE, latex_options = "hold_position") %>%
#column_spec(1, bold = TRUE) %>% collapse_rows(columns = 1, valign = "top")
}
## ----session-info-------------------------------------------------------------
sessionInfo()