HWTernaryPlot {HardyWeinberg}R Documentation

Ternary plot with the Hardy-Weinberg acceptance region

Description

HWTernaryPlot is a routine that draws a ternary plot for three-way genotypic compositions (AA,AB,BB), and represents the acceptance region for different tests for Hardy-Weinberg equilibrium (HWE) in the plot. This allows for graphical testing of a large set of markers (e.g. SNPs) for HWE. The (non) significance of the test for HWE can be inferred from the position of the marker in the ternary plot. Different statistical tests for HWE can be done graphically with this routine: the ordinary chisquare test, the chisquare test with continuity correction and the Fisher exact test.

Usage

HWTernaryPlot(X, n = NA, addmarkers = TRUE, newframe = TRUE, hwcurve = TRUE, 
vbounds = TRUE, mafbounds = FALSE, mafvalue = 0.05, axis = 0, region = 1, 
vertexlab = colnames(X), alpha = 0.05, vertex.cex = 1, pch = 19, cc = 0.5, 
markercol = "black", markerbgcol = "black", cex = 0.75, axislab = "", 
verbose = FALSE, markerlab = NULL, mcex = 1, connect = FALSE, curvecols = 
rep("black",5), signifcolour = TRUE, curtyp = "solid", ssf = "max", ...)

Arguments

X a matrix of n genotypic compositions or counts. If it is a matrix of compositions, X should have (n rows that sum 1, and 3 columns, with the relative frequencies of AA, AB and BB respectively. Argument n should be supplied as well. If X is a matrix of raw genotypic counts, it should have 3 columns with the absolute counts of AA, AB and BB respectively. Argument n may be supplied and will be used for painting acceptance regions. If not supplied n is computed from the data in X.
n the samples size (for a complete composition with no missing data).
addmarkers represent markers by dots in the triangle (addmarkers=TRUE) or not
(addmarkers=FALSE).
newframe allows for plotting additional markers in an already existing ternary plot. Overplotting is achieved by setting newframe to FALSE. Setting newframe = TRUE (default) will create a new ternary plot.
hwcurve draw the HW parabola in the plot (hwcurve=TRUE) or not (hwcurve=FALSE).
vbounds indicate the area corresponding to expected counts > 5 (vbounds=TRUE) or not (vbounds=FALSE).
mafbounds indicate the area corresponding to MAF < mafvalue.
mafvalue a critical value for the minor allele frequency (MAF).
axis draw a vertex axis
0 = no axis is drawn
1 = draw the AA axis
2 = draw the AB axis
3 = draw the BB axis
region the type of acceptance region to be delimited in the triangle
0 = no acceptance region is drawn
1 = draw the acceptance region corresponding to a Chi-square test
2 = draw the acceptance region corresponding to a Chi-square test with continuity correction
3 = draw the acceptance region corresponding to a Chi-square test with continuity correction for D > 0
4 = draw the acceptance region corresponding to a Chi-square test with continuity correction for D < 0
5 = draw the acceptance regions for all preceding tests simultaneously
6 = draw the acceptance region corresponding to a Chi-square test with continuity correction with the upper limit for D > 0 and the lower limit for D < 0
7 = draw the acceptance region corresponding to a two-sided Fisher exact test
vertexlab labels for the three vertices of the triangle
alpha significance level (0.05 by default)
vertex.cex character expansion factor for the labels of the vertices of the triangle.
pch the plotting character used to represent the markers.
cc value for the continuity correction parameter (0.5 by default).
markercol vector with colours for the marker points in the triangle.
markerbgcol vector with background colours for the marker points in the triangle.
cex expansion factor for the marker points in the triangle.
axislab a label to be put under the horizontal axis.
verbose print information on the numerically found cut-points between curves of the acceptance region and the edges of the triangle.
markerlab labels for the markers in the triangle.
mcex character expansion factor for the labels of the markers in the ternary plot.
connect connect the represented markers by a line in the ternary plot.
curvecols a vector with four colour specifications for the different curves that can be used to delimit the HW acceptance region. E.g. curvecols=c("red", "green","blue","black","purple") will paint the Hardy-Weinberg curve red, the limits of the acceptance region for an ordinary chi-square test for HWE green, the limits of the acceptance region for a chi-square test with continuity correction when D > 0 blue and the limits of the acceptance region for a chi-square test with continuity correction when D < 0 black, and the limits of the FE acceptance region purple.
signifcolour colour the marker points automatically according to the result of a signifance test (green markers non-siginficant, red markers significant). signifcolour only takes effect if region is set to 1, 2 or 7.
curtyp style of the drawn curves ("dashed","solid","dotted",...)
ssf sample size function ("max","min","mean","median",...). Indicates how the sample size for drawing acceptance regions is determined from the matrix of counts.
... other arguments passed on to the plot function (e.g. main for a main title).

Value

minp minimum allele frequency above which testing for HWE is appropriate (expected counts exceeding 5).
maxp maximum allele frequency below which testing for HWE is appropriate.
inrange number of markers in the appropriate range.
percinrange percentage of markers in the appropriate.
nsignif number of significant markers (only if region equals 1,2 or 7.)

Author(s)

Jan Graffelman jan.graffelman@upc.edu

References

Graffelman, J. and Morales, J. (2008) Graphical tests for Hardy-Weinberg equilibrium based on the ternary plot. Human Heredity 65(2):77-84.

See Also

HWChisq

Examples


n <- 100 # sample size
m <- 100 # number of markers

out <- HWData(n,m)
Xc <- out$Xc
Xa <- out$Xt

HWTernaryPlot(Xc,100,region=1,hwcurve=TRUE,vbounds=FALSE,vertex.cex=2,Xa=Xa)

[Package HardyWeinberg version 1.3 Index]