Package 'trackViewer'

Title: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data
Description: Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.
Authors: Jianhong Ou [aut, cre] , Julie Lihua Zhu [aut]
Maintainer: Jianhong Ou <[email protected]>
License: GPL (>= 2)
Version: 1.43.5
Built: 2024-12-11 03:19:55 UTC
Source: https://github.com/bioc/trackViewer

Help Index

Minimal designed plotting tool for genomic data

Description

A package that plot data and annotation information along genomic coordinates in an elegance style. This tool is based on Gviz but want to draw figures in minimal style for publication.

Author(s)

Maintainer: Jianhong Ou [email protected] (ORCID)

Authors:

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
trs <- geneModelFromTxdb(TxDb.Hsapiens.UCSC.hg19.knownGene,
                         org.Hs.eg.db,
                         chrom="chr11", 
                         start=122929275, 
                         end=122930122)
extdata <- system.file("extdata", package="trackViewer",
                       mustWork=TRUE)
repA <- importScore(paste(extdata, "cpsf160.repA_+.wig", sep="/"),
                    paste(extdata, "cpsf160.repA_-.wig", sep="/"),
                    format="WIG")
strand(repA@dat) <- "+"
strand(repA@dat2) <- "-"
fox2 <- importScore(paste(extdata, "fox2.bed", sep="/"), format="BED")
dat <- coverageGR(fox2@dat)
fox2@dat <- dat[strand(dat)=="+"]
fox2@dat2 <- dat[strand(dat)=="-"]
gr <- GRanges("chr11", IRanges(122929275, 122930122), strand="-")
vp <- viewTracks(trackList(repA, fox2, trs), gr=gr, autoOptimizeStyle=TRUE)
addGuideLine(c(122929767, 122929969), vp=vp)
addArrowMark(list(x=unit(.5, "npc"), 
                  y=unit(.39, "npc")),
             col="blue")

Add arrow mark to the figure at a given position

Description

A function to add arrow mark for emphasizing peaks

Usage

addArrowMark(
  pos = grid.locator(),
  label = NULL,
  angle = 15,
  length = unit(0.25, "inches"),
  col = "red",
  cex = 1,
  quadrant = 4,
  type = "closed",
  vp = NULL
)

Arguments

pos

A unit object representing the location of arrow mark to be placed at current viewport. Default is the value of grid.locator, which will get the location of the mouse click.
label

A character or expression vector.
angle

A parameter passed into grid::arrow function. The angle of arrow head in degrees (smaller numbers produce narrower, pointier arrows). Essentially describes the width of the arrow head.
length

A parameter passed into grid::arrow function. Aunit specifying the length of the arrow head.
col

color of the arrow
cex

Multiplier applied to fontsize
quadrant

the direction of arrow, 1: to bottomleft, 2: to bottomright, 3: to topright, 4: to topleft
type

A parameter passed into grid::arrow function. One of "open" or "closed" indicating whether the arrow head should be a closed triangle.
vp

A Grid viewport object. It must be output of viewTracks

Value

invisible x, y position value.

See Also

See Also as addGuideLine, arrow

Examples

grid.newpage()
addArrowMark(list(x=unit(.5, "npc"), 
               y=unit(.5, "npc")), 
               label="label1",
               col="blue")
##  how to get the position by mouse click
if(interactive()){
pos <- addArrowMark(label="byClick")
addArrowMark(pos, label="samePosAsAbove")
}

Add guide lines to the tracks

Description

A function to add lines for emphasizing the positions

Usage

addGuideLine(guideLine, col = "gray", lty = "dashed", lwd = 1, vp = NULL)

Arguments

guideLine

The genomic coordinates to draw the lines
col

A vector for the line color
lty

A vector for the line type
lwd

A vector for the line width
vp

A Grid viewport object. It must be output of viewTracks

See Also

See Also as getCurTrackViewport, addArrowMark, viewTracks

Examples

vp <- getCurTrackViewport(trackViewerStyle(), 10000, 10200)
addGuideLine(c(10010, 10025, 10150), vp=vp)

Add annotation markers to the figure at a given position

Description

A function to add annotation markers for emphasizing interactions

Usage

addInteractionAnnotation(
  obj,
  idx,
  FUN = grid.polygon,
  panel = c("top", "bottom"),
  ...
)

Arguments

obj

A GInteractions object, GRanges object or numeric vector. For numeric vector, the positive value will generate a line with slope 1 and negative value will generate a line at the position with slope -1.
idx

The layer number of track.
FUN

Function for plot. Available functions are grid.polygon, grid.lines, and grid.text for GInteractions object; grid.lines, and grid.text for GRanges object; FUN is not used for numeric vector.
panel

Plot regions. Available values are "top", "bottom".
...

Parameters will be passed to FUN.

Value

invisible viewport for plot region.

See Also

See Also as addGuideLine, addArrowMark

Examples

library(trackViewer)
library(InteractionSet)
gi <- readRDS(system.file("extdata", "nij.chr6.51120000.53200000.gi.rds",
 package="trackViewer"))
tads <- GInteractions(
GRanges("chr6", 
        IRanges(c(51130001, 51130001, 51450001, 52210001), width = 20000)),
GRanges("chr6", 
        IRanges(c(51530001, 52170001, 52210001, 53210001), width = 20000)))
range <- GRanges("chr6", IRanges(51120000, 53200000))
tr <- gi2track(gi)
viewTracks(trackList(tr), 
           gr=range, autoOptimizeStyle = TRUE)
addInteractionAnnotation(tads, "tr", grid.lines,
 gp=gpar(col = "#E69F00", lwd=3, lty=3))

Aggregate Region Analysis

Description

Extract the interaction signal means from given coordinates.

Usage

ARA(gr, upstream = 2e+05, downstream = upstream, resolution = 10000, ...)

Arguments

gr

A 'GRanges' object. The center of the object will be used for alignment for all the given regions.
upstream, downstream

numeric(1L). Upstream and downstream from the center of given 'gr' input will be used to extract the signals.
resolution

numeric(1L). The resolution will be passed to importGInteractions function.
...

The parameters used by importGInteractions function. Please note that the ranges resolution and out parameter should not be involved.

Value

A GInteractions object with scores which represent the mean values of the interactions.

Examples

hic <- system.file("extdata", "test_chr22.hic", package = "trackViewer",
                   mustWork=TRUE)
gr <- GRanges("22", c(seq(20000001, 50000001, by=10000000), width=1))
gi <- ARA(gr, file=hic, format="hic")
rg <- GRanges("22", IRanges(1, 400000))
op <- optimizeStyle(trackList(gi2track(gi)))
heatmap <- op$tracks
sty <- op$style
setTrackViewerStyleParam(sty, "xat", c(1, 200000, 400000))
setTrackViewerStyleParam(sty, "xlabel",c("-20K", "center", "20K"))
viewTracks(heatmap, viewerStyle=sty, gr=rg)

browse tracks

Description

browse tracks by a web browser.

Usage

browseTracks(
  trackList,
  gr = GRanges(),
  ignore.strand = TRUE,
  width = NULL,
  height = NULL,
  ...
)

Arguments

trackList

an object of trackList
gr

an object of GRanges
ignore.strand

ignore the strand or not when do filter. default TRUE
width

width of the figure
height

height of the figure
...

parameters not used

Value

An object of class htmlwidget that will intelligently print itself into HTML in a variety of contexts including the R console, within R Markdown documents, and within Shiny output bindings.

Examples

extdata <- system.file("extdata", package="trackViewer", mustWork=TRUE)
files <- dir(extdata, "-.wig")
tracks <- lapply(paste(extdata, files, sep="/"), 
                 importScore, format="WIG")
tracks <- lapply(tracks, function(.ele) {strand(.ele@dat) <- "-"; .ele})
names(tracks) <- c("trackA", "trackB")
fox2 <- importScore(paste(extdata, "fox2.bed", sep="/"), format="BED")
dat <- coverageGR(fox2@dat)
fox2@dat <- dat[strand(dat)=="+"]
fox2@dat2 <- dat[strand(dat)=="-"]
gr <- GRanges("chr11", IRanges(122929275, 122930122))
browseTracks(trackList(tracks, fox2), gr=gr)

Shiny bindings for browseTracks

Description

Output and render functions for using browseTracks within Shiny applications and interactive Rmd documents.

Usage

browseTracksOutput(outputId, width = "100%", height = "600px")

renderbrowseTracks(expr, env = parent.frame(), quoted = FALSE)

Arguments

outputId

output variable to read from
width, height

Must be a valid CSS unit (like '100%', '400px', 'auto') or a number, which will be coerced to a string and have 'px' appended.
expr

An expression that generates a browseTracks
env

The environment in which to evaluate expr.
quoted

Is expr a quoted expression (with quote())? This is useful if you want to save an expression in a variable.

calculate coverage

Description

calculate coverage for GRanges, GAlignments or GAlignmentPairs

Usage

coverageGR(gr)

Arguments

gr

an object of RGanges, GAlignments or GAlignmentPairs

Value

an object of GRanges

See Also

See Also as coverage, coverage-methods

Examples

bed <- system.file("extdata", "fox2.bed", package="trackViewer",
                   mustWork=TRUE)
fox2 <- importScore(bed)
fox2$dat <- coverageGR(fox2$dat)

dandelion.plots

Description

Plot variants and somatic mutations

Usage

dandelion.plot(
  SNP.gr,
  features = NULL,
  ranges = NULL,
  type = c("fan", "circle", "pie", "pin"),
  newpage = TRUE,
  ylab = TRUE,
  ylab.gp = gpar(col = "black"),
  xaxis = TRUE,
  xaxis.gp = gpar(col = "black"),
  yaxis = FALSE,
  yaxis.gp = gpar(col = "black"),
  legend = NULL,
  cex = 1,
  maxgaps = 1/50,
  heightMethod = NULL,
  label_on_feature = FALSE,
  ...
)

Arguments

SNP.gr

A object of GRanges or GRangesList. All the width of GRanges must be 1.
features

A object of GRanges or GRangesList.
ranges

A object of GRanges or GRangesList.
type

Character. Could be fan, circle, pie or pin.
newpage

plot in the new page or not.
ylab

plot ylab or not. If it is a character vector, the vector will be used as ylab.
ylab.gp, xaxis.gp, yaxis.gp

An object of class gpar for ylab, xaxis or yaxis.
xaxis, yaxis

plot xaxis/yaxis or not. If it is a numeric vector with length greater than 1, the vector will be used as the points at which tick-marks are to be drawn. And the names of the vector will be used to as labels to be placed at the tick points if it has names.
legend

If it is a list with named color vectors, a legend will be added.
cex

cex will control the size of circle.
maxgaps

maxgaps between the stem of dandelions. It is calculated by the width of plot region divided by maxgaps. If a GRanges object is set, the dandelions stem will be clustered in each genomic range.
heightMethod

A function used to determine the height of stem of dandelion. eg. Mean. Default is length.
label_on_feature

Labels of the feature directly on them. Default FALSE.
...

not used.

Details

In SNP.gr and features, metadata of the GRanges object will be used to control the color, fill, border, height, data source of pie if the type is pie.

Examples

SNP <- c(10, 100, 105, 108, 400, 410, 420, 600, 700, 805, 840, 1400, 1402)
SNP.gr <- GRanges("chr1", IRanges(SNP, width=1, names=paste0("snp", SNP)), 
                  score=sample.int(100, length(SNP))/100)
features <- GRanges("chr1", IRanges(c(1, 501, 1001), 
                                    width=c(120, 500, 405),
                                    names=paste0("block", 1:3)),
                    color="black",
                    fill=c("#FF8833", "#51C6E6", "#DFA32D"),
                    height=c(0.1, 0.05, 0.08))
dandelion.plot(SNP.gr, features, type="fan")

Prepare gene model from an object of TxDb

Description

Generate an object of track for viewTracks by given parameters.

Usage

geneModelFromTxdb(
  txdb,
  orgDb,
  gr,
  chrom,
  start,
  end,
  strand = c("*", "+", "-"),
  txdump = NULL
)

Arguments

txdb

An object of TxDb
orgDb

An object of "OrgDb"
gr

An object of GRanges.
chrom

chromosome name, must be a seqname of txdb
start

start position
end

end position
strand

strand
txdump

output of as.list(txdb), a list of data frames that can be used to make the db again with no loss of information.

Value

Generate a list of track from a TxDb object.

See Also

See Also as importScore, importBam, viewTracks

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
trs <- geneModelFromTxdb(TxDb.Hsapiens.UCSC.hg19.knownGene,
                         org.Hs.eg.db,
                         chrom="chr20", 
                         start=22560000, 
                         end=22565000, 
                         strand="-")

track from TxDb

Description

Generate a track object from TxDb by given gene ids

Usage

geneTrack(ids, txdb, symbols, type = c("gene", "transcript"), asList = TRUE)

Arguments

ids

Gene IDs. A vector of character. It should be keys in txdb.
txdb

An object of TxDb.
symbols

symbol of genes.
type

Output type of track, "gene" or "transcript".
asList

Output a list of tracks or not. Default TRUE.

Value

An object of track

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
ids <- c("3312", "390259", "341056", "79827")
symbols <- mget(ids, org.Hs.egSYMBOL)
geneTrack(ids, TxDb.Hsapiens.UCSC.hg19.knownGene, symbols)

Get current track viewport

Description

Get current track viewport for addGuideLine

Usage

getCurTrackViewport(curViewerStyle, start, end)

Arguments

curViewerStyle

an object of trackViewerStyle
start

start position of current track
end

end position of current track

Value

an object of viewport

See Also

See Also as addGuideLine

Examples

vp <- getCurTrackViewport(trackViewerStyle(), 10000, 10200)
addGuideLine(c(10010, 10025, 10150), vp=vp)

get gene ids by genomic location

Description

retrieve gene ids from txdb object by genomic location.

Usage

getGeneIDsFromTxDb(gr, txdb)

Arguments

gr

GRanges object.
txdb

An object of TxDb.

Value

A character vector of gene ids

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
gr <- parse2GRanges("chr11:122,830,799-123,116,707")
ids <- getGeneIDsFromTxDb(gr, TxDb.Hsapiens.UCSC.hg19.knownGene)

get genomic location by gene symbol

Description

given a gene name, get the genomic coordinates.

Usage

getLocation(symbol, txdb, org)

Arguments

symbol

Gene symbol
txdb

txdb will be used to extract the genes
org

org package name

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
getLocation("HSPA8", TxDb.Hsapiens.UCSC.hg19.knownGene, "org.Hs.eg.db")

convert GInteractions to track object

Description

Convert GInteractions object to track object

Usage

gi2track(gi, gi2)

Arguments

gi

an object of GInteractions
gi2

an object of GInteractions

Value

an track object

Examples

gi <- readRDS(system.file("extdata", "nij.chr6.51120000.53200000.gi.rds", package="trackViewer"))
gi2track(gi)

color sheme for the schema for Chromosome Band (Ideogram)

Description

Describe the colors of giemsa stain results

Usage

gieStain()

Value

A character vector of colors

Examples

gieStain()

GInteractions operator

Description

GInteractions operations (add, aubtract, multiply, divide)

Usage

GIoperator(gi_list, col = "score", operator = c("+", "-", "*", "/"))

Arguments

gi_list

a list of GInteractions objects
col

colname of metadata to be calculated
operator

operator, "+" means A + B, and so on. User-defined function also could be used.

Value

an object of GInteractions

Examples

library(InteractionSet)
gr2 <- GRanges(seqnames=c("chr1", "chr1"),
               ranges=IRanges(c(7,13), width=3))
gr3 <- GRanges(seqnames=c("chr1", "chr1"),
               ranges=IRanges(c(1, 4), c(3, 9)))
gi <- GInteractions(gr2, gr3, score=c(1, 2))
gi2 <- GInteractions(gr2, gr3, score=c(3, 4))
GIoperator(list(gi, gi2), col="score", operator="+")
GIoperator(list(gi, gi2), col="score", operator="-")

plot GRanges metadata

Description

plot GRanges metadata for different types

Usage

gridPlot(gr, gp, type, xscale)

Arguments

gr

an object of GRanges with metadata. All metadata must be numeric.
gp

an object of gpar
type

type of the figure, could be barplot, line, point and heatmap
xscale

x scale of the viewport

GRanges operator

Description

GRanges operations (add, aubtract, multiply, divide)

Usage

GRoperator(
  A,
  B,
  col = "score",
  operator = c("+", "-", "*", "/", "^", "%%"),
  ignore.strand = TRUE
)

Arguments

A

an object of GRanges
B

an object of GRanges
col

colname of A and B to be calculated
operator

operator, "+" means A + B, and so on. User-defined function also could be used.
ignore.strand

When set to TRUE, the strand information is ignored in the overlap calculations.

Value

an object of GRanges

Examples

gr2 <- GRanges(seqnames=c("chr1", "chr1"),
ranges=IRanges(c(7,13), width=3),
strand=c("-", "-"), score=3:4)
gr3 <- GRanges(seqnames=c("chr1", "chr1"),
               ranges=IRanges(c(1, 4), c(3, 9)),
               strand=c("-", "-"), score=c(6L, 2L))
GRoperator(gr2, gr3, col="score", operator="+")
GRoperator(gr2, gr3, col="score", operator="-")
GRoperator(gr2, gr3, col="score", operator="*")
GRoperator(gr2, gr3, col="score", operator="/")
GRoperator(gr2, gr3, col="score", operator=mean)

plot ideogram with data

Description

plot ideogram with data for multiple chromosomes

Usage

ideogramPlot(
  ideo,
  dataList,
  layout = NULL,
  horiz = TRUE,
  parameterList = list(vp = plotViewport(margins = c(0.1, 4.1, 0.3, 0.1)), ideoHeight =
    unit(1/(1 + length(dataList)), "npc"), vgap = unit(0.3, "lines"), ylabs = "auto",
    ylabsRot = ifelse(horiz, 0, 90), ylabsPos = unit(2.5, "lines"), xaxis = FALSE, yaxis
    = FALSE, xlab = "", types = "barplot", heights = NULL, dataColumn = "score", gps =
    gpar(col = "black", fill = "gray")),
  colorSheme = gieStain(),
  gp = gpar(fill = NA, lwd = 2),
  ...
)

Arguments

ideo

output of loadIdeogram.
dataList

a GRangesList of data to plot.
layout

The layout of chromosomes. Could be a list with chromosome names as its elements.
horiz

a logical value. If FALSE, the ideograms are drawn vertically to the left. If TRUE, the ideograms are drawn horizontally at the bottom.
parameterList

a list of parameters for each dataset in the dataList. The elements of the parameters could be xlabs, ylabs, etc. type could be barplot, line, point, heatmap.
colorSheme

A character vector of giemsa stain colors.
gp

parameters used for grid.roundrect.
...

parameters not used.

Examples

## Not run: 
ideo <- loadIdeogram("hg38")
library(rtracklayer)
library(grid)
dataList <- ideo
dataList$score <- as.numeric(dataList$gieStain)
dataList <- dataList[dataList$gieStain!="gneg"]
dataList <- GRangesList(dataList)
grid.newpage()
ideogramPlot(ideo, dataList, 
             layout=list("chr1", "chr2", c("chr3", "chr22"), 
                         c("chr4", "chr21"), c("chr5", "chr20"), 
                         c("chr6", "chr19"), c("chr7", "chr18"),
                         c("chr8", "chr17"), c("chr9", "chr16"),
                         c("chr10", "chr15"), c("chr11", "chr14"),
                         c("chr12", "chr13"), c("chrX", "chrY")),
             parameterList = list(types="heatmap", colorKeyTitle="sample1"))

## End(Not run)

Reading data from a BAM file

Description

Read a track object from a BAM file

Usage

importBam(file, file2, ranges = GRanges(), pairs = FALSE)

Arguments

file

The path to the BAM file to read.
file2

The path to the second BAM file to read.
ranges

An object of GRanges to indicate the range to be imported
pairs

logical object to indicate the BAM is paired or not. See readGAlignments

Value

a track object

See Also

See Also as importScore, track, viewTracks

Examples

bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
mustWork=TRUE)
dat <- importBam(file=bamfile, ranges=GRanges("seq1", IRanges(1, 50), strand="+"))

Reading data from a BED or WIG file to RleList

Description

Read a track object from a BED, bedGraph, WIG or BigWig file to RleList

Usage

importData(files, format = NA, ranges = GRanges())

Arguments

files

The path to the files to read.
format

The format of import file. Could be BAM, BED, bedGraph, WIG or BigWig
ranges

An object of GRanges to indicate the range to be imported

Value

a list of RleList.

Examples

#import a BED file
bedfile <- system.file("tests", "test.bed", package="rtracklayer",
                       mustWork=TRUE)
dat <- importData(files=bedfile, format="BED",
                  ranges=GRanges("chr7", IRanges(127471197, 127474697)))

##import a WIG file
wigfile <- system.file("tests", "step.wig", package = "rtracklayer",
                       mustWork=TRUE)
dat <- importData(files=wigfile, format="WIG", 
                  ranges=GRanges("chr19", 
                                 IRanges(59104701, 59110920)))

##import a BigWig file
if(.Platform$OS.type!="windows"){
  ##this is because we are using rtracklayer::import
  bwfile <- system.file("tests", "test.bw", package = "rtracklayer",
                        mustWork=TRUE)
  dat <- importData(files=bwfile, format="BigWig", 
                    ranges=GRanges("chr19", IRanges(1500, 2700)))
}

Reading data from a ginteractions, hic, cool, or validPairs file

Description

Read a track object from a ginteractions, hic, mcool, or validPairs file

Usage

importGInteractions(
  file,
  format = c("ginteractions", "hic", "cool", "validPairs"),
  ranges = GRanges(),
  ignore.strand = TRUE,
  out = c("track", "GInteractions"),
  resolution = 1e+05,
  unit = c("BP", "FRAG"),
  normalization = c("NONE", "VC", "VC_SQRT", "KR", "SCALE", "GW_KR", "GW_SCALE", "GW_VC",
    "INTER_KR", "INTER_SCALE", "INTER_VC", "balanced"),
  matrixType = c("observed", "oe", "expected"),
  ...
)

Arguments

file

The path to the file to read.
format

The format of import file. Could be ginteractions, hic, cool or validPairs
ranges

An object of GRanges to indicate the range to be imported. For .hic file, if the length of ranges is 2, the first range will be used as anchor 1 and the second range will be used as anchor 2.
ignore.strand

ignore the strand or not when do filter. default TRUE
out

output format. Default is track. Possible values: track, GInteractions.
resolution

Resolutions for the interaction data.
unit

BP (base pair) or FRAG (fragment) (.hic file only).
normalization

Type of normalization, NONE, VC, VC_SORT or KR for .hic and NONE, balanced for .cool.
matrixType

Type of matrix for .hic file. Available choices are "observed", "oe", and "expected". default is "observed".
...

NOT used.

Value

a track object

See Also

See Also as listResolutions, listChromosomes, readHicNormTypes

Examples

#import a ginteractions file
#gi <- system.file("extdata", "test.ginteractions.tsv", package="trackViewer",
#                       mustWork=TRUE)
#dat <- importGInteractions(file=gi, format="ginteractions",
#                   ranges=GRanges("chr7", IRanges(127471197, 127474697)))

##import a hic file
if(.Platform$OS.type!="windows"){
hic <- system.file("extdata", "test_chr22.hic", package = "trackViewer",
                       mustWork=TRUE)
dat <- importGInteractions(file=hic, format="hic", 
                           ranges=GRanges("22", IRanges(1500000, 100000000)))
}

##import a cool file
cool <- system.file("extdata", "test.mcool", package = "trackViewer",
                     mustWork=TRUE)
dat <- importGInteractions(file=cool, format="cool",
                           resolution = 2,
                           ranges=GRanges("chr1", IRanges(10, 28)))

##import a validPairs file
#validPairs <- system.file("extdata", "test.validPairs", package = "trackViewer",
#                       mustWork=TRUE)
#dat <- importGInteractions(file=validPairs, format="validPairs")

Reading data from a BED or WIG file

Description

Read a track object from a BED, bedGraph, WIG or BigWig file

Usage

importScore(
  file,
  file2,
  format = c("BED", "bedGraph", "WIG", "BigWig"),
  ranges = GRanges(),
  ignore.strand = TRUE
)

Arguments

file

The path to the file to read.
file2

The path to the second file to read.
format

The format of import file. Could be BED, bedGraph, WIG or BigWig
ranges

An object of GRanges to indicate the range to be imported
ignore.strand

ignore the strand or not when do filter. default TRUE

Value

a track object

See Also

See Also as importBam, track, viewTracks

Examples

#import a BED file
bedfile <- system.file("tests", "test.bed", package="rtracklayer",
                       mustWork=TRUE)
dat <- importScore(file=bedfile, format="BED",
                   ranges=GRanges("chr7", IRanges(127471197, 127474697)))

##import a WIG file
wigfile <- system.file("tests", "step.wig", package = "rtracklayer",
                       mustWork=TRUE)
dat <- importScore(file=wigfile, format="WIG")

##import a BigWig file
if(.Platform$OS.type!="windows"){##this is because we are using rtracklayer::import
  bwfile <- system.file("tests", "test.bw", package = "rtracklayer",
                        mustWork=TRUE)
  dat <- importScore(file=bwfile, format="BigWig")
}

##import 2 file
wigfile1 <- system.file("extdata", "cpsf160.repA_+.wig", package="trackViewer",
                        mustWork=TRUE)
wigfile2 <- system.file("extdata", "cpsf160.repA_-.wig", package="trackViewer",
                        mustWork=TRUE)
dat <- importScore(wigfile1, wigfile2, format="WIG", 
                   ranges=GRanges("chr11", IRanges(122817703, 122889073)))

plot tracks for single cell RNAseq

Description

Plot single cell RNAseq data as heatmap track for Seurat object.

Usage

importScSeqScore(
  object,
  files,
  samplenames,
  ...,
  txdb,
  gene,
  id,
  idents,
  gr,
  color,
  withCoverageTrack = TRUE,
  flag = scanBamFlag(isSecondaryAlignment = FALSE, isUnmappedQuery = FALSE,
    isNotPassingQualityControls = FALSE, isSupplementaryAlignment = FALSE)
)

Arguments

object

Seurat object.
files

bam file to be scanned.
samplenames

sample names for files.
...

parameters used by readGAlignmentsList or readGAlignments
txdb

TxDb object for gene model.
gene

Gene name to plot. (row value)
id

The id of gene used in txdb.
idents

indentity class to define the groups to plot. (column value)
gr

GRanges object to define the ploting region.
color

vector of colors used in heatmap.
withCoverageTrack

plot coverage track or not.
flag

An integer(2) vector used to filter reads based on their 'flag' entry.

Examples

## Not run: 
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
test_file <- "https://github.com/10XGenomics/subset-bam/raw/master/test/test.bam"
trs <- importScSeqScore(files=test_file, 
                        txdb=TxDb.Hsapiens.UCSC.hg19.knownGene,
                        id="653635", gene = "WASH7P")

## End(Not run)

List the available chromosome

Description

List the chromosomes available in the file.

Usage

listChromosomes(file, format = c("hic", "cool"))

Arguments

file

character(1). File name of .hic or .cool/.mcool/.scool
format

character(1). File format, "hic" or "cool".

Examples

hicfile <- system.file("extdata", "test_chr22.hic", package="trackViewer")
listChromosomes(hicfile)
coolfile <- system.file("extdata", "test.mcool", package="trackViewer")
listChromosomes(coolfile, format="cool")

List the available normalizations

Description

List the normalizations available in the file.

Usage

listNormalizations(file, format = c("hic", "cool"))

Arguments

file

character(1). File name of .hic or .cool/.mcool/.scool
format

character(1). File format, "hic" or "cool".

Examples

hicfile <- system.file("extdata", "test_chr22.hic", package="trackViewer")
listNormalizations(hicfile)
coolfile <- system.file("extdata", "test.mcool", package="trackViewer")
listNormalizations(coolfile, format="cool")

List the available resolutions

Description

List the resolutions available in the file.

Usage

listResolutions(file, format = c("hic", "cool"))

Arguments

file

character(1). File name of .hic or .cool/.mcool/.scool
format

character(1). File format, "hic" or "cool".

Examples

hicfile <- system.file("extdata", "test_chr22.hic", package="trackViewer")
listResolutions(hicfile)
coolfile <- system.file("extdata", "test.mcool", package="trackViewer")
listResolutions(coolfile, format="cool")

load ideogram from UCSC

Description

Download ideogram table from UCSC

Usage

loadIdeogram(genome, chrom = NULL, ranges = NULL, ...)

Arguments

genome

Assembly name assigned by UCSC, such as hg38, mm10.
chrom

A character vector of chromosome names, or NULL.
ranges

A Ranges object with the intervals.
...

Additional arguments to pass to the GRanges constructor.

Value

A GRanges object.

See Also

See Also as ideogramPlot

Examples

## Not run: 
head(loadIdeogram("hg38", chrom = "chr1"))

## End(Not run)

Lolliplots

Description

Plot variants and somatic mutations

Usage

lolliplot(
  SNP.gr,
  features = NULL,
  ranges = NULL,
  type = "circle",
  newpage = TRUE,
  ylab = TRUE,
  ylab.gp = gpar(col = "black"),
  yaxis = TRUE,
  yaxis.gp = gpar(col = "black"),
  xaxis = TRUE,
  xaxis.gp = gpar(col = "black"),
  legend = NULL,
  legendPosition = "top",
  cex = 1,
  dashline.col = "gray80",
  jitter = c("node", "label"),
  rescale = FALSE,
  label_on_feature = FALSE,
  lollipop_style_switch_limit = 10,
  ...
)

Arguments

SNP.gr

A object of GRanges, GRangesList or a list of GRanges. All the width of GRanges must be 1.
features

A object of GRanges, GRangesList or a list of GRanges. The metadata 'featureLayerID' are used for drawing features in different layers. See details in vignette.
ranges

A object of GRanges or GRangesList.
type

character. Could be circle, pie, pin, pie.stack or flag.
newpage

Plot in the new page or not.
ylab

Plot ylab or not. If it is a character vector, the vector will be used as ylab.
ylab.gp, xaxis.gp, yaxis.gp

An object of class gpar for ylab, xaxis or yaxis.
yaxis

Plot yaxis or not.
xaxis

Plot xaxis or not. If it is a numeric vector with length greater than 1, the vector will be used as the points at which tick-marks are to be drawn. And the names of the vector will be used to as labels to be placed at the tick points if it has names.
legend

If it is a list with named color vectors, a legend will be added.
legendPosition

The position of legend. Possible positions are 'top', 'right', and 'left'.
cex

cex will control the size of circle.
dashline.col

color for the dashed line.
jitter

jitter the position of nodes or labels.
rescale

logical(1), character(1), numeric vector, or a dataframe with rescale from and to. Rescalse the x-axis or not. if dataframe is used, colnames must be from.start, from.end, to.start, to.end. And the from scale must cover the whole plot region. The rescale parameter can be set as "exon" or "intron" to emphasize "exon" or "intron" region. The "exon" or "intron" can be followed with an integer e.g. "exon_80", or "intron_99". The integer indicates the total percentage of "exon" or "intron" region. Here "exon" indicates all regions in features. And "intron" indicates all flank regions of the features.
label_on_feature

Labels of the feature directly on them. Default FALSE.
lollipop_style_switch_limit

The cutoff value for lollipop style for the 'circle' type. If the max score is greater than this cutoff value, trackViewer will only plot one shape at the highest score. Otherwise trackViewer will draw the shapes like 'Tanghulu'.
...

not used.

Details

In SNP.gr and features, metadata of the GRanges object will be used to control the color, fill, border, alpha, shape, height, cex, dashline.col, data source of pie if the type is pie. And also the controls for labels by name the metadata start as label.parameter.<properties>, and for node labels by name the metadata start as node.label.<properties>, such as label.parameter.rot, label.parameter.gp. The parameter is used for grid.text.or plotMotifLogoA. The metadata 'featureLayerID' for features are used for drawing features in different layers. The metadata 'SNPsideID' for SNP.gr are used for determining the side of lollipops. And the 'SNPsideID' could only be 'top' or 'bottom'.

Examples

SNP <- c(10, 100, 105, 108, 400, 410, 420, 600, 700, 805, 840, 1400, 1402)
x <- sample.int(100, length(SNP))
SNP.gr <- GRanges("chr1", IRanges(SNP, width=1, names=paste0("snp", SNP)), 
                  value1=x, value2=100-x)
SNP.gr$color <- rep(list(c("red", 'blue')), length(SNP))
SNP.gr$border <- sample.int(7, length(SNP), replace=TRUE)
features <- GRanges("chr1", IRanges(c(1, 501, 1001), 
                                    width=c(120, 500, 405),
                                    names=paste0("block", 1:3)),
                    color="black",
                    fill=c("#FF8833", "#51C6E6", "#DFA32D"),
                    height=c(0.1, 0.05, 0.08),
                    label.parameter.rot=45)
lolliplot(SNP.gr, features, type="pie")

Optimize the style of plot

Description

Automatic optimize the stlye of trackViewer

Usage

optimizeStyle(trackList, viewerStyle = trackViewerStyle(), theme = NULL)

Arguments

trackList

An object of trackList
viewerStyle

An object of trackViewerStyle
theme

A character string. Could be "bw", "col" or "safe".

Value

a list of a trackList and a trackViewerStyle

See Also

See Also as viewTracks

Examples

extdata <- system.file("extdata", package="trackViewer",
                       mustWork=TRUE)
files <- dir(extdata, ".wig")
tracks <- lapply(paste(extdata, files, sep="/"), 
                 importScore, format="WIG")
re <- optimizeStyle(trackList(tracks))
trackList <- re$tracks
viewerStyle <- re$style

parse text into GRanges

Description

parse text like "chr13:99,443,451-99,848,821:-" into GRanges

Usage

parse2GRanges(text)

Arguments

text

character vector like "chr13:99,443,451-99,848,821:-" or "chr13:99,443,451-99,848,821"

Value

an object of GRanges

Examples

parse2GRanges("chr13:99,443,451-99,848,821:-")

convert WIG format track to BED format track

Description

convert WIG format track to BED format track for a given range

Usage

parseWIG(trackScore, chrom, from, to)

Arguments

trackScore

an object of track with WIG format
chrom

sequence name of the chromosome
from

start coordinate
to

end coordinate

Value

an object of track

Examples

extdata <- system.file("extdata", package="trackViewer", mustWork=TRUE)
repA <- importScore(file.path(extdata, "cpsf160.repA_-.wig"),
                    file.path(extdata, "cpsf160.repA_+.wig"),
                    format="WIG")
strand(repA$dat) <- "-"
strand(repA$dat2) <- "+"
parseWIG(repA, chrom="chr11", from=122929275, to=122930122)

plot GRanges data

Description

A function to plot GRanges data for given range

Usage

plotGRanges(
  ...,
  range = GRanges(),
  viewerStyle = trackViewerStyle(),
  autoOptimizeStyle = FALSE,
  newpage = TRUE
)

Arguments

...

one or more objects of GRanges
range

an object of GRanges
viewerStyle

an object of trackViewerStyle
autoOptimizeStyle

should use optimizeStyle to optimize style
newpage

should be draw on a new page?

Value

An object of viewport for addGuideLine

See Also

See Also as addGuideLine, addArrowMark

Examples

gr1 <- GRanges("chr1", IRanges(1:50, 51:100))
gr2 <- GRanges("chr1", IRanges(seq(from=10, to=80, by=5),
                               seq(from=20, to=90, by=5)))
vp <- plotGRanges(gr1, gr2, range=GRanges("chr1", IRanges(1, 100)))
addGuideLine(guideLine=c(5, 10, 50, 90), col=2:5, vp=vp)

gr <- GRanges("chr1", IRanges(c(1, 11, 21, 31), width=9), 
              score=c(5, 10, 5, 1))
plotGRanges(gr, range=GRanges("chr1", IRanges(1, 50)))

plot ideogram

Description

plot ideogram for one chromosome

Usage

plotIdeo(
  ideo,
  chrom = seqlevels(ideo)[1],
  colorSheme = gieStain(),
  gp = gpar(fill = NA),
  ...
)

Arguments

ideo

output of loadIdeogram.
chrom

A length 1 character vector of chromosome name.
colorSheme

A character vector of giemsa stain colors.
gp

parameters used for grid.roundrect.
...

parameters not used.

Examples

## Not run: 
ideo <- loadIdeogram("hg38")
library(grid)
grid.newpage()
plotIdeo(ideo)

## End(Not run)

plot ideogram with data for one chromosome

Description

plot ideogram with data for one chromosome

Usage

plotOneIdeo(
  ideo,
  dataList,
  parameterList = list(vp = plotViewport(margins = c(0.1, 4.1, 1.1, 0.1)), ideoHeight =
    unit(1/(1 + length(dataList)), "npc"), vgap = unit(1, "lines"), ylabs =
    seqlevels(ideo)[1], ylabsRot = 90, ylabsPos = unit(2.5, "lines"), xaxis = FALSE,
    yaxis = FALSE, xlab = "", types = "barplot", heights = NULL, dataColumn = "score",
    gps = gpar(col = "black", fill = "gray")),
  chrom = seqlevels(ideo)[1],
  colorSheme = gieStain(),
  gp = gpar(fill = NA, lwd = 2),
  ...
)

Arguments

ideo

output of loadIdeogram.
dataList

a GRangesList of data to plot.
parameterList

a list of parameters for each dataset in the dataList. The elements of the parameters could be xlabs, ylabs, etc. type could be barplot, line, point, heatmap.
chrom

A length 1 character vector of chromosome name.
colorSheme

A character vector of giemsa stain colors.
gp

parameters used for grid.roundrect.
...

parameters not used.

Examples

## Not run: 
ideo <- loadIdeogram("hg38")
library(rtracklayer)
library(grid)
dataList <- ideo[seqnames(ideo) %in% "chr1"]
dataList$score <- as.numeric(dataList$gieStain)
dataList <- dataList[dataList$gieStain!="gneg"]
dataList <- GRangesList(dataList, dataList)
grid.newpage()
plotOneIdeo(ideo, dataList, chrom="chr1")

## End(Not run)

Class "pos"

Description

An object of class "pos" represents a point location

Slots

x

A numeric value, indicates the x position

y

A numeric value, indicates the y position

unit

"character" apecifying the units for the corresponding numeric values. See unit

Reduce method for 'GInteractions'

Description

Reduce returns an object of the same type as x containing reduced ranges for each distinct (seqname, strand) pairing.

Usage

## S4 method for signature 'GInteractions'
reduce(x, min.gapwidth = 1L, ignore.strand = TRUE, ...)

Arguments

x

GInteractions object.
min.gapwidth

Ranges separated by a gap of at least min.gapwidth positions are not merged.
ignore.strand

TRUE or FALSE. Whether the strand of the input ranges should be ignored or not.
...

Not used.

Examples

## Not run: 
library(InteractionSet) 
gi <- readRDS(system.file("extdata", "gi.rds", package="trackViewer"))
reduce(head(gi, n=20))

## End(Not run)

List of tracks

Description

An extension of List that holds only track objects.

Usage

## S4 replacement method for signature 'trackList'
seqlevelsStyle(x) <- value

trackList(..., heightDist = NA)

Arguments

x

trackList object.
value

values to be assigned.
...

Each tracks in ... becomes an element in the new trackList, in the same order. This is analogous to the list constructor, except every argument in ... must be derived from track.
heightDist

A vector or NA to define the height of each track.

See Also

track.

Class "trackStyle"

Description

An object of class "trackStyle" represents track style.

An object of class "track" represents scores of a given track.

Usage

## S4 method for signature 'track'
seqlevels(x)

## S4 method for signature 'track'
seqlevelsStyle(x)

## S4 replacement method for signature 'track'
seqlevelsStyle(x) <- value

## S4 method for signature 'track'
show(object)

## S4 method for signature 'track'
x$name

## S4 replacement method for signature 'track'
x$name <- value

setTrackStyleParam(ts, attr, value)

## S4 method for signature 'track,character'
setTrackStyleParam(ts, attr, value)

setTrackXscaleParam(ts, attr, value)

## S4 method for signature 'track,character'
setTrackXscaleParam(ts, attr, value)

setTrackYaxisParam(ts, attr, value)

## S4 method for signature 'track,character'
setTrackYaxisParam(ts, attr, value)

Arguments

x

an object of trackStyle or track
value

values to be assigned.
object

an object of trackStyle.
name

slot name of trackStyle or track
ts

An object of track.
attr

the name of slot of trackStyle object to be changed.

Details

The attr of setTrackXscaleParam could not only be a slot of xscale, but also be position. If the attr is set to position, value must be a list of x, y and label. For example setTrackXscaleParam(track, attr="position", value=list(x=122929675, y=4, label=500))

Slots

tracktype

"character" track type, could be peak, line, histogram, or annotation. Default is "peak". "annotation" is used to mark the peak regions. For interaction data, it could be "heatmap" or "link".

color

"character" track color. If the track has dat and dat2 slot, it should have two values.

NAcolor

"character" NA color for interactionData.

breaks

"numeric" breaks for color keys of interactionData.

height

"numeric" track height. It should be a value between 0 and 1

marginTop

"numeric" track top margin

marginBottom

"numeric" track bottom margin

xscale

object of xscale, describe the details of x-scale

yaxis

object of yaxisStyle, describe the details of y-axis

ylim

"numeric" y-axis range

ylabpos

"character", ylable postion, ylabpos should be 'left', 'right', 'topleft', 'bottomleft', 'topright', 'bottomright', 'abovebaseline', 'underbaseline', or 'none'. For gene type track, it also could be 'upstream' or 'downstream'

ylablas

"numeric" y lable direction. It should be a integer 0-3. See par:las

ylabgp

A "list" object, It will convert to an object of class gpar. This is basically a list of graphical parameter settings of y-label.

ysplit

A "numeric" to split y plot region for interaction data. Default is 0.5, which will split the region half to half. It will only work for back to back plot.

dat

Object of class GRanges the scores of a given track. It should contain score metadata.

dat2

Object of class GRanges the scores of a given track. It should contain score metadata. When dat2 and dat is paired, dat will be drawn as positive value where dat2 will be drawn as negative value (-1 * score)

type

The type of track. It could be 'data', 'gene', 'transcript', 'scSeq', 'lollipopData' or 'interactionData'.

format

The format of the input. It could be "BED", "bedGraph", "WIG", "BigWig" or "BAM"

style

Object of class trackStyle

name

unused yet

See Also

Please try to use importScore and importBam to generate the object.

Examples

extdata <- system.file("extdata", package="trackViewer",
mustWork=TRUE)
fox2 <- importScore(file.path(extdata, "fox2.bed"), format="BED")
setTrackStyleParam(fox2, "color", c("red","green"))
setTrackXscaleParam(fox2, "gp", list(cex=.5))
setTrackYaxisParam(fox2, "gp", list(col="blue"))
fox2$dat <- GRanges(score=numeric(0))

Class "trackViewerStyle"

Description

An object of class "trackViewerStyle" represents track viewer style.

Usage

trackViewerStyle(...)

setTrackViewerStyleParam(tvs, attr, value)

## S4 method for signature 'trackViewerStyle,character'
setTrackViewerStyleParam(tvs, attr, value)

Arguments

...

Each argument in ... becomes an slot in the new trackViewerStyle.
tvs

An object of trackViewerStyle.
attr

the name of slot to be changed.
value

values to be assigned.

Slots

margin

"numeric", specify the bottom, left, top and right margin.

xlas

"numeric", label direction of x-axis mark. It should be a integer 0-3. See par:las

xgp

A "list", object, It will convert to an object of class gpar. This is basically a list of graphical parameter settings of x-axis. For y-axis, see yaxisStyle

xaxis

"logical", draw x-axis or not

xat

"numeric", the values will be passed to grid.xaxis as 'at' parameter.

xlabel

"character", the values will be passed to grid.xaxis as 'label' parameter.

autolas

"logical" automatic determine y label direction

flip

"logical" flip the x-axis or not, default FALSE

Examples

tvs <- trackViewerStyle()
setTrackViewerStyleParam(tvs, "xaxis", TRUE)

plot tracks based on gene name

Description

given a gene name, plot the tracks.

Usage

viewGene(
  symbol,
  filenames,
  format,
  txdb,
  org,
  upstream = 1000,
  downstream = 1000,
  anchor = c("gene", "TSS"),
  plot = FALSE
)

Arguments

symbol

Gene symbol
filenames

files used to generate tracks
format

file format used to generate tracks
txdb

txdb will be used to extract the genes
org

org package name
upstream

upstream from anchor
downstream

downstream from anchor
anchor

TSS, or gene
plot

plot the tracks or not.

Value

an invisible list of a trackList, a trackViewerStyle and a GRanges

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
extdata <- system.file("extdata", package="trackViewer", mustWork=TRUE)
filename = file.path(extdata, "fox2.bed")
optSty <- viewGene("HSPA8", filenames=filename, format="BED", 
                   txdb=TxDb.Hsapiens.UCSC.hg19.knownGene, 
                   org="org.Hs.eg.db")

plot the tracks

Description

A function to plot the data for given range

Usage

viewTracks(
  trackList,
  chromosome,
  start,
  end,
  strand,
  gr = GRanges(),
  ignore.strand = TRUE,
  viewerStyle = trackViewerStyle(),
  autoOptimizeStyle = FALSE,
  newpage = TRUE,
  operator = NULL,
  smooth = FALSE,
  lollipop_style_switch_limit = 10
)

Arguments

trackList

an object of trackList
chromosome

chromosome
start

start position
end

end position
strand

strand
gr

an object of GRanges
ignore.strand

ignore the strand or not when do filter. default TRUE
viewerStyle

an object of trackViewerStyle
autoOptimizeStyle

should use optimizeStyle to optimize style
newpage

should be draw on a new page?
operator

operator, could be +, -, *, /, ^, %%, and NA. "-" means dat - dat2, and so on. NA means do not apply any operator. Note: if multiple operator is supplied, please make sure the length of operator keep same as the length of trackList.
smooth

logical(1) or numeric(). Plot smooth curve or not. If it is numeric, eg n, mean of nearby n points will be used for plot. If it is numeric, the second number will be the color. Default coloer is 2 (red).
lollipop_style_switch_limit

The cutoff value for lollipop style for the 'circle' type. If the max score is greater than this cutoff value, trackViewer will only plot one shape at the highest score. Otherwise trackViewer will draw the shapes like 'Tanghulu'.

Value

An object of viewport for addGuideLine

See Also

See Also as addGuideLine, addArrowMark

Examples

extdata <- system.file("extdata", package="trackViewer",
                       mustWork=TRUE)
files <- dir(extdata, "-.wig")
tracks <- lapply(paste(extdata, files, sep="/"), 
                 importScore, format="WIG")
tracks <- lapply(tracks, function(.ele) {strand(.ele@dat) <- "-"; .ele})
fox2 <- importScore(paste(extdata, "fox2.bed", sep="/"), format="BED")
dat <- coverageGR(fox2@dat)
fox2@dat <- dat[strand(dat)=="+"]
fox2@dat2 <- dat[strand(dat)=="-"]
gr <- GRanges("chr11", IRanges(122929275, 122930122), strand="-")
viewTracks(trackList(track=tracks, fox2=fox2), gr=gr, autoOptimizeStyle=TRUE)

Class "xscale"

Description

An object of class "xscale" represents x-scale style.

Slots

from

A pos class, indicates the start point postion of x-scale.

to

A pos class, indicates the end point postion of x-scale.

label

"character" the label of x-scale

gp

A "list" object, It will convert to an object of class gpar. This is basically a list of graphical parameter settings of x-scale.

draw

A "logical" value indicating whether the x-scale should be draw.

Class "yaxisStyle"

Description

An object of class "yaxisStyle" represents y-axis style.

Slots

at

"numeric" vector of y-value locations for the tick marks

label

"logical" value indicating whether to draw the labels on the tick marks.

gp

A "list" object, It will convert to an object of class gpar. This is basically a list of graphical parameter settings of y-axis.

draw

A "logical" value indicating whether the y-axis should be draw.

main

A "logical" value indicating whether the y-axis should be draw in left (TRUE) or right (FALSE).