Description Usage Arguments Examples
View source: R/plotPWCoancestry.R
fineSTRUCTURE pairwise coancestry plot
1 2 | plotPWCoancestry(x, cex = 0.5, colours = NULL, keep_ones = FALSE,
max_coancestry = NULL)
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x |
a |
cex |
(default=0.7) number indicating the amount by which plotting text and symbols should be scaled relative to the default. |
colours |
a vector of colors to be passed to image. (e.g., heat.colors(n=200)[200:1]) |
keep_ones |
(default=FALSE) whether or not to annotate node with full support. |
max_coancestry |
the maximum value to be reprsented in the heatmap. Large values will be reduced to max_coancestry. |
1 2 3 4 5 6 7 8 | # fineStruct example
chunkfile <- system.file("extdata/fine_structure_files", "EastAsiaSimple.EMlinked.chunkcounts.out", package = "starmie")
treefile <- system.file("extdata/fine_structure_files", "EastAsiaSimple.EMlinked.tree.xml", package = "starmie")
mcmcfile <- system.file("extdata/fine_structure_files", "EastAsiaSimple.EMlinked.mcmc.xml", package = "starmie")
meancoincidencefile <- system.file("extdata/fine_structure_files", "EastAsiaSimple.EMlinked.meancoincidence.csv", package = "starmie")
mappopchunkfile <- system.file("extdata/fine_structure_files", "EastAsiaSimple.EMlinked.mapstate.csv", package = "starmie")
fineData <- loadFineStructure(chunkfile, treefile, mcmcfile, meancoincidencefile, mappopchunkfile)
plotPWCoancestry(fineData, max_coancestry=500)
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