qmatrix | R Documentation |
Get the Q
ancestry coefficient matrix computed by the tess3 function.
qmatrix(tess3, K, rep = "best")
tess3 |
a tess3 object. |
K |
number of ancestral populations. |
rep |
an integer indicating which run to display (default = lowest error run). |
a Q
matrix of ancestry coefficients from a specified run.
tess3
barplot.tess3Q
plot.tess3Q
CreatePalette
library(tess3r)
# load Arabidopsis data
data(data.at)
# Running tess3
obj <- tess3(data.at$X, coord = data.at$coord, K = 5,
ploidy = 1, method = "projected.ls", openMP.core.num = 4)
# Get the ancestry matrix
Q.matrix <- qmatrix(obj, K = 5)
# Plot the barplot
barplot(Q.matrix, border = NA, space = 0, xlab = "Individuals",
ylab = "Ancestry proportions", main = "Ancestry matrix") -> bp
axis(1, at = 1:nrow(Q.matrix), labels = bp$order, las = 3, cex.axis = .4)
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