plot_ViolinRuns function

Violin plot of run length per individual (either sum or mean)

Function to produce violin plots of the distribution of runs lengths per group The sum of run lengths, or its average, per individual sample is used to characterize the distribution of runs

plot_ViolinRuns(runs, method = c("sum", "mean"), outputName = NULL,
  plotTitle = NULL, savePlots = FALSE)

Arguments

• runs: a data.frame with runs per individual (group, id, chrom, nSNP, start, end, length)
• method: "sum" or "mean" of run lengths per individual samples
• 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

Violin plot of the distribution of runs-lengths (sum or mean)

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_ViolinRuns(runs = runsDF, method = "sum" , savePlots = FALSE)
plot_ViolinRuns(runs = runsDF, method = "mean" , savePlots = FALSE)