Ideogram {ggbio} | R Documentation

## Plot single chromosome with cytoband

### Description

Plot single chromosome with cytoband.

### 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)

### 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.

### 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)

[Package ggbio version 1.26.1 Index]