plotAbs {PureCN} | R Documentation |
This function provides various plots for finding correct purity and ploidy
combinations in the results of a runAbsoluteCN
call.
plotAbs( res, id = 1, type = c("hist", "overview", "BAF", "AF", "all"), chr = NULL, germline.only = TRUE, show.contour = FALSE, purity = NULL, ploidy = NULL, alpha = TRUE, show.segment.means = c("SNV", "segments", "both"), max.mapping.bias = 0.8, palette.name = "Paired", col.snps = "#2b6391", col.chr.shading = "#f0f0f0", ... )
res |
Return object of the |
id |
Candidate solutions to be plotted. |
type |
Different types of plots. |
chr |
If |
germline.only |
If |
show.contour |
For |
purity |
Display expected integer copy numbers for purity, defaults to
purity of the solution ( |
ploidy |
Display expected integer copy numbers for ploidy, defaults to
ploidy of the solution ( |
alpha |
Add transparency to the plot if VCF contains many variants
(>2000, |
show.segment.means |
Show segment means in germline allele frequency
plot? If |
max.mapping.bias |
Exclude variants with high mapping bias from
plotting. Note that bias is reported on an inverse scale; a variant with
mapping bias of 1 has no bias. ( |
palette.name |
The default |
col.snps |
The color used for germline SNPs. |
col.chr.shading |
The color used for shading alternate chromosomes. |
... |
Additonal parameters passed to the |
Returns NULL
.
Markus Riester
data(purecn.example.output) plotAbs(purecn.example.output, type="overview") # plot details for the maximum likelihood solution (rank 1) plotAbs(purecn.example.output, 1, type="hist") plotAbs(purecn.example.output, 1, type="BAF") plotAbs(purecn.example.output, 1, type = "BAF", chr="chr2")