ggbio (version 1.16.1)

Ideogram: Plot single chromosome with cytoband

Description

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

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, cytoband = TRUE, aspect.ratio = 1/20, genome)
## constructor
Ideogram(obj, subchr = NULL, which = NULL, xlabel = FALSE, cytoband = TRUE, color = "red", fill = "red", alpha = 0.7, zoom.region = NULL, zoom.offset = 0.2, size = 1, aspect.ratio = 1/20, ..., genome)
## depricated
plotSingleChrom(obj, subchr = NULL, zoom.region, xlab, ylab, main, xlabel = FALSE, color = "red", fill = "red", alpha = 0.7, zoom.offset = 0.1, size = 1, cytoband = TRUE, aspect.ratio = 1/20, genome)

Arguments

obj

A GenomicRanges object, which include extra information about cytoband, 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.

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

...

passed to ggbio constructor.

Value

A ggplot object.

Details

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

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)