R: Plot single chromosome with cytoband

plotSingleChrom {ggbio}

R Documentation

Plot single chromosome with cytoband

Description

Plot single chromosome with cytoband. plotIdeogram is synonyms to plotSingleChrom.

Usage

plotSingleChrom(obj, subchr, zoom.region, xlab, ylab, main, xlabel =
                 FALSE, color = "red", fill = "red", alpha = 0.7,
                 cytoband = TRUE, aspect.ratio = NULL, genome)

plotIdeogram(obj, subchr, zoom.region, xlab, ylab, main, xlabel =
                 FALSE, color = "red", fill = "red", alpha = 0.7,
                 cytoband = TRUE, aspect.ratio = NULL, genome)

Arguments

`obj`	A `GenomicRanges` object, which include extra information about cytoband, check biovizBase::isIdeogram.
`subchr`	A single character of chromosome names to show.
`zoom.region`	A numeric vector of length 2 indicating zoomed region.
`xlab`	Label for x
`ylab`	Label for y
`main`	Title for plot.
`xlabel`	A logical value. Show the x label or not.
`color`	color for highlight region.
`fill`	fill color for highlight region.
`alpha`	alpha for highlight regio.
`cytoband`	If FALSE, plot just blank chromosome without cytoband. default is TRUE. es
`aspect.ratio`	aspect ratio for the chromosome ideogram plot, default is NULL.
`genome`	genome character passed to `getIdeogram`

Details

User could provide the whole ideogram and use subchr to point to particular chromosome.

Value

A ggplot object.

Author(s)

Tengfei Yin

Examples

## Not run: 
##D library(biovizBase)
##D data(hg19IdeogramCyto, package = "biovizBase")
##D biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE
##D plotIdeogram(hg19IdeogramCyto, "chr1")
##D plotIdeogram(hg19IdeogramCyto, "chr1", xlabel = TRUE)
##D ## zoom
##D plotIdeogram(hg19IdeogramCyto, "chr1",  zoom.region = c(1e8, 1.5e8))
## End(Not run)

[Package ggbio version 1.5.20 ]