chromosome.viewlinkage {lodplot} | R Documentation |
Pretty plot of location score versus genetic map position on one (human) chromosome
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, ...)
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. |
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).
A grid graphical object.
David L Duffy