plotPWCoancestry: fineSTRUCTURE pairwise coancestry plot

Description Usage Arguments Examples

View source: R/plotPWCoancestry.R

Description

fineSTRUCTURE pairwise coancestry plot

Usage

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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

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# 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.