plot_InbreedingChr {detectRUNS}

Plot Froh-based inbreeding coefficients by group

Description

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.

Usage

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)?

Value

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')