plotSingleChrom: Plot single chromosome with cytobands

In tengfei/ggbio: Visualization tools for genomic data

Plot single chromosome with cytobands

Description

Plot single chromosome with cytobands.

Usage

plotIdeogram(obj, subchr = NULL, zoom.region = NULL, which = NULL, xlab, ylab, main, xlabel =
                 FALSE, color = "red", fill = "red", alpha = 0.7,
                 zoom.offset = 0.2, size = 1,
                 cytobands = TRUE, aspect.ratio = 1/20, genome)

## constructor
Ideogram(obj, subchr = NULL, which = NULL, xlabel = FALSE,
                 cytobands = TRUE, color = "red", fill = "red", alpha =
                 0.7, zoom.region = NULL, zoom.offset = 0.2, size = 1,
                 aspect.ratio = 1/20, ..., genome)

Arguments

obj	A GenomicRanges object, which include extra information about cytobands, check biovizBase::isIdeogram.
subchr	A single character of chromosome names to show.
which	GRanges object to subset and highlight the ideogram.
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.
zoom.offset	zoomed highlights region offset around chromosome plotting region.
size	size for zoomed region rectangle boundary.
cytobands	If FALSE, plot just blank chromosome without cytobands. default is TRUE. es
aspect.ratio	aspect ratio for the chromosome ideogram plot, default is NULL.
genome	genome character passed to getIdeogram
...	passed to ggbio constructor.

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: 
library(biovizBase)
p.ideo <- Ideogram(genome = "hg19")
p.ideo
library(GenomicRanges)
p.ideo + xlim(GRanges("chr2", IRanges(1e8, 1e8+10000)))
Ideogram(genome = "hg19", xlabel = TRUE)

## End(Not run)

tengfei/ggbio documentation built on Nov. 5, 2023, 6:17 a.m.