`plotTreesAtSites`¶

call plotTreeFromBed at the sites in a site file; color individual nodes by allele

Description¶

call plotTreeFromBed at the sites in a site file; color individual nodes by allele

Usage¶

plotTreesAtSites(bedFile, sites, pos = NULL, start = NULL,
  end = NULL, doSingletons = FALSE, colors = list(A = "red", C =
  "green", G = "turquoise", T = "purple", N = "gray"), ...)

Arguments¶

Argument	Description
`bedFile`	bed.gz file from smc2bed with trees
`sites`	Sites object, as returned by readSites(). Will plot one tree for each site.
`pos`	If not NULL, a vector of integers giving which sites to plot. If NULL, plot all sites
`start`	start position
`end`	end position
`doSingletons`	whether to plot singletons
`colors`	Color to use for each allele in leaf of tree
`...`	Additional arguments passed to plotTreesFromBed