karyoDiploid: Diploid karyogram

In ibdsim2: Simulation of Chromosomal Regions Shared by Family Members

Diploid karyogram

Description

Show chromosomal segments in a diploid karyogram

Usage

karyoDiploid(
  paternal,
  maternal,
  chrom = 1:22,
  col = c(paternal = "lightblue", maternal = "orange"),
  alpha = 1,
  bgcol = "gray95",
  title = NULL
)

Arguments

paternal, maternal	data.frames (or objects coercible to data.frames) containing the segments to be shown on the paternal and maternal strands of the karyogram. The first three columns must contain chromosome (with or without "chr" prefix), start position and stop position (in Mb). Column names are ignored, as well as any further columns.
chrom	The (autosomal) chromosomes to be included in the plot, given as a subset of the integers 1, 2,..., 22.
col	A vector of two colours (in any form recognisable by R). If only one colour is given it is recycled. If the vector is named, a colour legend is included in the plot, using the names as labels.
alpha	A single numeric in ⁠[0,1]⁠ indicating colour transparency.
bgcol	The background colour of the chromosomes.
title	Plot title.

Value

The plot object is returned invisibly, so that additional ggplot layers may be added if needed.

Examples

## Not run: 
pat = data.frame(chrom = c(1,4,5,5,10,10), start = c(100,50,20,80,10,80),
                 end = c(120,100,25,100,70,120))
mat = data.frame(chrom = c(2,4,5,5,10), start = c(80,50,10,80,50),
                 end = c(120,100,35,100,120))
karyoDiploid(pat, mat)

## End(Not run)

ibdsim2 documentation built on Aug. 17, 2023, 5:17 p.m.