plot-bins-1d2d¶

This step produces alternate plots that show bins in terms of their computed read-depth ratios (RDR), B-allele frequencies (BAF), and cluster assignments. 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. These plots should be used to review the clustering and tune clustering parameters.

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

Input¶

plot-bins considers two different inputs which are tab-separated files, one is mandatory and the other is optional (required to show cluster centers):

A file of clustered genomic bins, specified with the flag -b, --bbc and with 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`

A file of clusters, which is required only by commands and it is specified through the flag -s, --segfile. The file has the following fields.

Field	Description
`ID`	The name of a cluster
`SAMPLE`	The name of a sample
`#BINS`	The number of bins included in `ID`
`RD`	The RDR of the cluster `ID` in `SAMPLE`
`#SNPS`	The total number of SNPs in the cluster `ID`
`COV`	The average coverage in the cluster `ID`
`ALPHA`	The alpha parameter of the binomial model for the BAF of the cluster `ID`
`BETA`	The beta parameter of the binomial model for the BAF of the cluster `ID`
`BAF`	The BAF of the cluster `ID` in `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)
`--rdrlim`	Axis limits for read-depth ratio	Specify limits as comma-separated values, e.g., '0,3'	None (determined by extremes of data)
`--centers`	Show cluster centers	Requires SEG file provided via `-s, --seg`. Enable by including this flag.	False
`--centromeres`	Mark centromere locations with grey rectangles	Enable by including this flag.	False
`-a, --alpha`	Opacity value for scatterplots	Valid values are (0, 1]. Smaller values make points more transparent.	1