chromosome.viewlinkage {lodplot}R Documentation

Produce a viewport with the chromosome along the top and a pendant lod score plot

Description

Pretty plot of location score versus genetic map position on one (human) chromosome

Usage

chromosome.viewlinkage(x, chrom, statistic = "lod", pheno.names = NULL, 
  min.stat = 0, max.stat = 4, col = 1:6, lwd = 2, lty = 1, 
  hpos = 0.85, width = 0.05, chromname.cex=1.5, 
  units = "cM", bands = "major", xticdist=50, 
  show.y.axis = FALSE, new = FALSE, ...)

Arguments

x is a data.frame containing variables chr (indicating the chromosome 1..X), pos (the map position, usually in cM), and the statistics to be plotted.
chrom is the chromosome to be plotted.
statistic is the vector of test statistics to be plotted, defaulting to "lod".
pheno.names gives a long name for the statistics, defaulting to the statistic name.
min.stat is the minimum plottable value of the statistic.
max.stat is the maximum plottable value of the statistic.
col is a vector of colours for the lod curve.
lty is a vector of line types for the lod curve.
lwd is a vector of line widths for the lod curve.
chromname.cex is relative font size for the chromosome label.
units are the map units, defaulting to "cM".
hpos is the Y coordinate for the chromosome ideogram
width is the width of the chromosome ideogram
bands is which chromosomal bands to display on the ideogram.
xticdist is the spacing of the X axis tickmarks, defaulting to 50.
show.y.axis determines whether the Y axis should be shown.
new indicates whether addition to existing plot.
... are other graphical parameters to be passed to plot.default.

Details

Given a set of genetic location scores and chromosomal positions, chromosome.viewlinkage produces a plot for chromosome chrom. A chromosome ideogram is drawn at the top of the plot, with band locations expressed on the same scale as the map positions (cM).

Value

A grid graphical object.

Author(s)

David L Duffy


[Package lodplot version 1.1 Index]