paintCytobands: Paint a chromosomal idiogram

In quantsmooth: Quantile smoothing and genomic visualization of array data

Description

Paints a human chromosomal idiogram in an existing plot Adapted from the paint.chromosome function in the lodplot package by David L Duffy

Usage

paintCytobands(chrom, pos = c(0, 0), units = "hg19", width = 0.4,
            length.out, bands = "major", orientation = c("h","v"), legend = TRUE,
            cex.leg = 0.7, bleach = 0, ...)

Arguments

chrom	chromosomal id, chromosome to plot 1:22,X,Y
pos	numeric vector of length 2, position in the plot to start the plot
units	character or data.frame, type of units for genomic data, or a dataframe with UCSC cytoband data, see lengthChromosome
width	numeric, width of the chromosome, the chromosome is plotted between pos[2] and pos[2]-width
length.out	numeric, if given, the chromosome will have this length in the plot
bands	if not equal to "major", then also the minor bands will be plotted
orientation	chromosome is plotted either Horizontally to the right of the starting point or Vertically down from the starting point
legend	logical, if TRUE then the bandnames are plotted next to the chromosome
cex.leg	numeric, relative size of legend text
bleach	numeric [0,1], proportion by which to bleach the chromosome
...	extra parameters for plot

Value

This function is executed for its side effects

Author(s)

David L Duffy , Jan Oosting

References

lodplot package

Examples

  plot(c(0,lengthChromosome(14,"bases")),c(-2,2),type="n",xaxt="n",yaxt="n",xlab="",ylab="")
  paintCytobands(14,units="bases")

quantsmooth documentation built on Nov. 8, 2020, 8:27 p.m.