Plots coexistent subpopulations determined by ExPANdS.
Usage
plotSPs(dm, sampleID=NA)
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.
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).