plot_StackedRuns: Plot stacked runs

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

Description

Function to plot stacked runs along the chromosome (signaling presence of large numbers of runs in specific regions of a chromosome) Counts on the y-axis, bps on the x-axis (position along the chromosome)

Usage

plot_StackedRuns(runs, savePlots = FALSE, separatePlots = FALSE,
  outputName = NULL)

Arguments

runs	a data.frame with runs per individual (group, id, chrom, nSNP, start, end, length)
savePlots	should plots be saved out in files (default) or plotted in the graphical terminal?
separatePlots	should plots for chromosomes be saved out to separate files?
outputName	title prefix (the base name of graph, if savePlots is TRUE)

Value

plot of stacked runs by population and by chromosome (pdf files)

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 runs per animal (interactive)
plot_StackedRuns(runs = runsDF, savePlots = FALSE, outputName = "ROHom")

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