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

In detectRUNS: Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes

Description

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

Usage

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)?

Value

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)

detectRUNS documentation built on Oct. 30, 2019, 11:41 a.m.