paintCytobands {quantsmooth}R Documentation

Paint a chromosomal idiogram

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 = c("cM", "bases", "ISCN"), 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 units along which to plot the chromosome
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 em{H}orizontally to the right of the starting point or em{V}ertically 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")


[Package quantsmooth version 1.8.0 Index]