kpPlotBigWig: kpPlotBigWig

In bernatgel/karyoploteR: Plot customizable linear genomes displaying arbitrary data

kpPlotBigWig

Description

Plots the wiggle values in a BigWig file. This function does not work on windows.

Usage

kpPlotBigWig(karyoplot, data, ymin=NULL, ymax="global", data.panel=1, r0=NULL, r1=NULL, col=NULL, border=NULL, clipping=TRUE, ...)

Arguments

karyoplot	(a KaryoPlot object) This is the first argument to all data plotting functions of karyoploteR. A KaryoPlot object referring to the currently active plot.
data	(a BigWigFile or character) The path to a bigwig file (either local or a URL to a remote file) or a BigWigFile object.
ymin	(numeric) The minimum value to be plotted on the data panel. If NULL, the minimum between 0 and the minimum value in the WHOLE GENOME will be used. (deafults to NULL)
ymax	(numeric or c("global", "per.chr", "visible.region")) The maximum value to be plotted on the data.panel. It can be either a numeric value or one of c("global", "per.chr", "per.region"). "Global" will set ymax to the maximum value in the whole data file. "per.chr" will set ymax to the maximum value in each chromosome. "visible.region" will set ymax to the maximum value in the visible region. (defaults to "global")
data.panel	(numeric) The identifier of the data panel where the data is to be plotted. The available data panels depend on the plot type selected in the call to plotKaryotype. (defaults to 1)
r0	(numeric) r0 and r1 define the vertical range of the data panel to be used to draw this plot. They can be used to split the data panel in different vertical ranges (similar to tracks in a genome browser) to plot differents data. If NULL, they are set to the min and max of the data panel, it is, to use all the available space. (defaults to NULL)
r1	(numeric) r0 and r1 define the vertical range of the data panel to be used to draw this plot. They can be used to split the data panel in different vertical ranges (similar to tracks in a genome browser) to plot differents data. If NULL, they are set to the min and max of the data panel, it is, to use all the available space. (defaults to NULL)
col	(color) The fill color of the area. A single color. If NULL the color will be assigned automatically, either a lighter version of the color used for the outer line or gray if the line color is not defined. If NA no area will be drawn. (defaults to NULL)
border	(color) The color of the line enclosing the area. A single color. If NULL the color will be assigned automatically, either a darker version of the color used for the area or black if col=NA. If NA no border will be drawn. (Defaults to NULL)
clipping	(boolean) Only used if zooming is active. If TRUE, the data representation will be not drawn out of the drawing area (i.e. in margins, etc) even if the data overflows the drawing area. If FALSE, the data representation may overflow into the margins of the plot. (defaults to TRUE)
...	The ellipsis operator can be used to specify any additional graphical parameters. Any additional parameter will be passed to the internal calls to the R base plotting functions.

Details

kpPlotBigWig plots the data contained in a binary file format called BigWig. BigWig are used to efficiently store numeric values computed for windows covering the whole genome, ususally the coverage from an NGS experiment such as ChIP-seq. Only data required for the plotted region is loaded, and when more than one chromosome is visible, it will load the data for one crhomosome at a time. The function accepts either a BigWigFile oject or a character with the path to a valid big wig file. The character can also be a URL to a remote server. In this case data will be loaded transparently using the import function from rtracklayer. The data is plotted using kpArea and therefore it is possible to plot as a single line, a line with shaded area below or as a shaded area only adjusting the col and border parameters.

Value

Returns the original karyoplot object with the data computed (ymax and ymin values used) stored at karyoplot$latest.plot

Note

Since this functions uses rtracklayer BigWig infrastructure and it does not work on windows, this function won't work on windows either.

See Also

plotKaryotype, kpArea, kpPlotBAMDensity

Examples

if (.Platform$OS.type != "windows") {
  bigwig.file <- system.file("extdata", "BRCA.genes.hg19.bw", package = "karyoploteR")
  brca.genes.file <- system.file("extdata", "BRCA.genes.hg19.txt", package = "karyoploteR")
  brca.genes <- toGRanges(brca.genes.file)
  seqlevelsStyle(brca.genes) <- "UCSC"

  kp <- plotKaryotype(zoom = brca.genes[1])
  kp <- kpPlotBigWig(kp, data=bigwig.file, r0=0, r1=0.2)
  kp <- kpPlotBigWig(kp, data=bigwig.file, r0=0.25, r1=0.45, border="red", lwd=2)
  kp <- kpPlotBigWig(kp, data=bigwig.file, r0=0.5, r1=0.7, ymin=0, ymax=1000, border="gold", col=NA)
  kpAxis(kp, r0=0.5, r1=0.7, ymin=0, ymax=1000)
  kp <- kpPlotBigWig(kp, data=bigwig.file, r0=0.75, r1=0.95, ymin=0, ymax="visible.region", border="orchid", col=NA)
  kpAxis(kp, r0=0.75, r1=0.95, ymin=0, ymax=kp$latest.plot$computed.values$ymax)
}

bernatgel/karyoploteR documentation built on Feb. 1, 2024, 11:48 p.m.