Description Usage Arguments Examples
Generates a heatmap of coverage for a subset of sequences. In the resulting heatmap, the color of a tile at coordinates (x, y) indicates the coverage of the sequence y in the individual x.
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data |
A table of coverage obtained with the |
popmap |
A population map obtained with the |
title |
Plot title (default NULL). |
males.color |
If a popmap is specified, sets the color of male individual names on the horizontal axis (default "dodgerblue3"). |
females.color |
If a popmap is specified, sets the color of female individual names on the horizontal axis (default "red3"). |
coverage.palette |
Color palette for coverage. The value should be a vector of length 5 corresponding to the following intervals/values: [0, 1 : mean, mean : 3rd quartile, 3rd quartile : (max - 1), max] (default c("white", "royalblue2", "black", "gold2", "red3")) |
individual.names |
If TRUE, shows individual names on the x-axis (default TRUE). |
sequence.names |
If TRUE, shows sequence names on the y-axis (defautl FALSE). |
individual.dendrogram |
If TRUE, shows individual clustering dendrogram on the x-axis (default TRUE). |
sequence.dendrogram |
If TRUE, shows sequence clustering dendrogram on the y-axis (default FALSE). |
1 2 3 4 5 6 | heatmap = coverage_heatmap(data, popmap = popmap,
title = "Individuals and sequences clustering based on coverage",
males.color = "blue", females.color = "red",
coverage.palette = c("white", "green", "black", "red", "red3"),
individual.names = TRUE, sequence.names = TRUE,
individual.dendrogram = TRUE, sequence.dendrogram = TRUE)
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