Plots coexistent subpopulations determined by ExPANdS.
Usage
plotSPs(dm, sampleID=NA, cex=0.5)
Arguments
dm
Matrix in which each row corrsponds to a point mutation (for example, the matrix output of assignMutations). Has to contain at least the following columnnames:
chr - the chromosome on which e
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 point mutation (x-axis) the function displays:
- the size of the subpopulation to which the mutation has been assigned (squares). Each square is colored based on the confidence with which the mutation has been assigned to the corresponding subpopulation (black - highest, white - lowest).
- the total ploidy of all alleles at the mutated genomic locus in that subpopulation (dots).
- 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).