plot_InbreedingChr function

Plot Froh-based inbreeding coefficients by group

The function plots the distribution of inbreeding/consanguinity coefficients per chromosome and/or group. Three types of plots can be produces: barplots, boxplots, violin plots. With style="All" all three plots are produced.

plot_InbreedingChr(runs, mapFile, groupSplit = TRUE,
  style = c("ChrBarPlot", "ChrBoxPlot", "FrohBoxPlot", "All"),
  outputName = NULL, plotTitle = NULL, savePlots = FALSE)

Arguments

• runs: R object (dataframe) with results on detected runs
• mapFile: Plink map file (for SNP position)
• groupSplit: plots split by group (defaults to TRUE)
• style: type of plot: ChrBarPlot, ChrBoxPlot, FrohBoxPlot, All (all plots)
• outputName: title prefix (the base name of graph, if savePlots is TRUE)
• plotTitle: title in plot (default NULL)
• savePlots: should plots be saved out to files or plotted in the graphical terminal (default)?

Returns

plots of the distribution of inbreeding by chromosome and group

Examples

# getting map and ped paths
genotypeFile <- system.file("extdata", "Kijas2016_Sheep_subset.ped", package = "detectRUNS")
mapFile <- system.file("extdata", "Kijas2016_Sheep_subset.map", package = "detectRUNS")

# calculating runs of Homozygosity
## Not run:

# skipping runs calculation
runs <- slidingRUNS.run(genotypeFile, mapFile, windowSize = 15, threshold = 0.1,  minSNP = 15,
ROHet = FALSE,  maxOppositeGenotype = 1, maxMiss = 1,  minLengthBps = 100000,  minDensity = 1/10000)
## End(Not run)

# loading pre-calculated data
runsFile <- system.file("extdata", "Kijas2016_Sheep_subset.sliding.csv", package="detectRUNS")
runsDF <- readExternalRuns(inputFile = runsFile, program = 'detectRUNS')

plot_InbreedingChr(runs = runsDF, mapFile = mapFile, style='All')