plot_Runs function

Function to plot runs per individual

Function to plot runs per individual (see Williams et al. 2016, Animal Genetics, for an example with animal data) Individual IDs on the y-axis, bps on the x-axis (position along the chromosome)

plot_Runs(runs, suppressInds = FALSE, savePlots = FALSE,
  separatePlots = FALSE, outputName = NULL)

Arguments

• runs: a data.frame with runs per individual (group, id, chrom, nSNP, start, end, length)
• suppressInds: shall we suppress individual IDs on the y-axis? (defaults to FALSE)
• savePlots: should plots be saved out to files (one pdf file for all chromosomes) or plotted in the graphical terminal (default)?
• separatePlots: should plots for each chromosome be saved out to separate files?
• outputName: title prefix (the base name of graph, if savePlots is TRUE)

Returns

plot of runs by chromosome

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_Runs(runs = runsDF, suppressInds = FALSE, savePlots = FALSE, outputName = "ROHom")