plotPWCoancestry: fineSTRUCTURE pairwise coancestry plot

In sa-lee/starmie: Population Structure Model Inference and Visualisation

Description

fineSTRUCTURE pairwise coancestry plot

Usage

plotPWCoancestry(x, cex = 0.5, colours = NULL, keep_ones = FALSE,
  max_coancestry = NULL)

Arguments

x	a fineStruct object
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.

Examples

# 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)

sa-lee/starmie documentation built on May 28, 2019, 11 a.m.