plot.scan {lodplot}R Documentation

Plot results of a linkage genome scan

Description

Produces several types of plot of the lod score (or other test statistic) versus genetic map position (cM) on each of 22 human autosomal chromosomes along with the X chromosome if requested. Decorates with a chromosome ideogram if appropriate.

Usage

plot.scan(x, type = "layout", statistic = "lod", with.X = TRUE, 
  min.lod = 0, max.lod = 4, pheno.names = NULL, units = "cM", 
  col = 1:6, lty = 1, lwd = 2, chromname.cex=0.9, ...)

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.
type is the type of plot: "layout", "linear", "overwrite", or "histogram", defaulting to "layout".
statistic is the test statistic to be plotted, defaulting to "lod".
with.X flags whether the X chromosome is to be included in the plot.
min.lod is the minimum plottable value of the statistic.
max.lod is the maximum plottable value of the statistic.
pheno.names gives a long name for the statistics, defaulting to the statistic name.
units are the map units, defaulting to "cM".
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 the relative font size for the chromosome label.
... are other graphical parameters to be passed to plot.default.

Details

Given a set of genetic location scores and chromosomal positions, plot.scan defaults to producing an array of plots ("layout"), one per chromosome, with each scaled to the chromosome length. A chromosome ideogram is drawn at the top of each plot, with band locations expressed on the same scale as the map positions (usually cM).

Alternatively, the "linear" option plots the entire genome on one graph, with divisions between the chromosomes. Chromosome ideograms are not added. The "overwrite" option overwrites the curves for each chromosome onto one graph, and the "histogram" option gives the distribution of lod scores over the entire sample.

The function uses the grid library. The ideogram band genetic map positions were interpolated from the physical positions of the bands estimated from the Build 35.1 human sequence for the NCBI Map Viewer.

Value

A grid type graphical object.

Author(s)

David L Duffy

References

Human chromosome ideograms. ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/maps/mapview/BUILD.35.1/ideogram.gz. Accessed September 2005.

Examples

# Plot one simulated scan
  plot.scan(halfsibscan(), col="red", with.X=TRUE)
# plot a genome scan
## Not run: x <-read.table("nfr.lod", h=T, na=".")
## Not run: 
plot.scan(x, statistic=c("flat.vc","flat.sqtl"), 
  col=c("red","blue"),with.X=TRUE)
## End(Not run)

[Package lodplot version 1.0 Index]