plot-cn-1d2d

This step produces alternate plots that show bins in terms of their computed read-depth ratios (RDR), B-allele frequencies (BAF), and assigned copy-number states. These plots show bins colored by cluster, where the color is consistent between the “2D” (RDR x BAF) view and the “1D” (genomic location x RDR/BAF) view. Additionally, the labeled points in the 2D plots and the black bars in the 1D plots show the expected positions of the assigned copy-number states (determined by the mixture proportions and fractional copy number scaling). These indicators can be used to evaluate the consistency of the HATCHet solution.

When plot_cn = True is indicated in hatchet.ini, both this command and the command plot-cn will be run.

These plots should be used to review the results of the copy-number assignment step compute_cn and tune its parameters. They are most useful when there are few samples - when there are many samples, the visualizations from plot-cn may be more interpretable.

Input

plot-bins requires a single tab-separated file as input. This file (e.g., best.bbc.ucn, results.diploid.n3.bbc.ucn.tsv, …) is typically produced by compute_cn and contains the following fields:

Field	Description
CHR	Name of a chromosome
START	Starting genomic position of a genomic bin in CHR
END	Ending genomic position of a genomic bin in CHR
SAMPLE	Name of a tumor sample
RD	RDR of the bin in SAMPLE
#SNPS	Number of SNPs present in the bin in SAMPLE
COV	Average coverage in the bin in SAMPLE
ALPHA	Alpha parameter related to the binomial model of BAF for the bin in SAMPLE, typically total number of reads from A allele
BETA	Beta parameter related to the binomial model of BAF for the bin in SAMPLE, typically total number of reads from B allele
BAF	BAF of the bin in SAMPLE
CLUSTER	The name of the corresponding cluster of the bin in SAMPLE
cn_normal	The copy number state of the normal diploid clone equal to 1|1
u_normal	The normal admixture of the normal diploid cells in the corresponding sample
cn_clone${n}	The copy number state of the ${n} tumor clone in the format A|B where A and B are the two allele-specific copy numbers of the corresponding genomic bin
u_clone${n}	The clone proportion of the ${n} tumor clone in the corresponding sample

Parameters

Name	Description	Usage	Default
-O, --outdir	Output directory	Directory in which output plots will be stored	"" (current directory)
--baflim	Axis limits for mirrored BAF	Specify limits as comma-separated values, e.g., '0,0.51'	None (determined by extremes of data)
--fcnlim	Axis limits for fractional copy numbers	Specify limits as comma-separated values, e.g., '0,3'	None (determined by extremes of data)
--centromeres	Mark centromere locations with grey rectangles	Enable by including this flag with no argument.	False
--bysample	Split plots into distinct sample-specific files (instead of grouping all 1D plots together and all 2D plots together)	Enable by including this flag with no argument.	False