Plots coexistent subpopulations determined by ExPANdS.
Usage
plotSPs(dm, sampleID=NA, cex=0.5)
Arguments
dm
Matrix in which each row corrsponds to a mutation (for example, the matrix output by assignMutations). Has to contain at least the following columnnames:
chr - the chrmosome on which each mut
sampleID
The name of the sample in which the mutations have been detected.
cex
The amount by which plotting text and symbols should be magnified relative to the default. See also help(par).
Value
For each mutation (x-axis) the function displays:
- the subpopulation to which the mutation has been assigned (squares),
- the ploidy of the locus in that subpopulation and
- the allele frequency of the mutation.
Allele frequencies and ploidities are colored based on the chromosome on which the mutation is located (stars - somatic mutations, triangles - loss of heterozygosity). Subpopulations are colored based on the confidence with which the mutation has been assigned to the corresponding subpopulation (black - highest, white - lowest).