NAME
cnvkit_scatter - Plot probe log2 coverages and segmentation calls together.
DESCRIPTION
usage: cnvkit.py scatter [-h] [-s FILENAME] [-c RANGE] [-g GENE]
- [-l RANGE_LIST] [-w WIDTH] [-o FILENAME]
-
[-a CHARACTER] [--by-bin] [--segment-color SEGMENT_COLOR] [--title TITLE] [-t] [--y-max Y_MAX] [--y-min Y_MIN] [--fig-size WIDTH HEIGHT] [-v FILENAME] [-i SAMPLE_ID] [-n NORMAL_ID] [-m MIN_VARIANT_DEPTH] [-z [ALT_FREQ]] [filename]
positional arguments:
- filename
-
Processed bin-level copy ratios (*.cnr), the output of the 'fix' sub-command.
options:
- -h, --help
-
show this help message and exit
- -s FILENAME, --segment FILENAME
-
Segmentation calls (.cns), the output of the 'segment' command.
- -c RANGE, --chromosome RANGE
-
Chromosome or chromosomal range, e.g. 'chr1' or 'chr1:2333000-2444000', to display. If a range is given, all targeted genes in this range will be shown, unless -g/--gene is also given.
- -g GENE, --gene GENE
-
Name of gene or genes (comma-separated) to display.
- -l RANGE_LIST, --range-list RANGE_LIST
-
File listing the chromosomal ranges to display, as BED, interval list or 'chr:start-end' text. Creates focal plots similar to -c/--chromosome for each listed region, combined into a multi-page PDF. The output filename must also be specified (-o/--output).
- -w WIDTH, --width WIDTH
-
Width of margin to show around the selected gene(s) (-g/--gene) or small chromosomal region (-c/--chromosome). [Default: 1000000]
- -o FILENAME, --output FILENAME
-
Output PDF file name.
Plot aesthetics:
- -a CHARACTER, --antitarget-marker CHARACTER
-
Plot antitargets using this symbol when plotting in a selected chromosomal region (-g/--gene or -c/--chromosome). [Default: same as targets]
- --by-bin
-
Plot data x-coordinates by bin indices instead of genomic coordinates. All bins will be shown with equal width, no blank regions will be shown, and x-axis values indicate bin number (within chromosome) instead of genomic position.
- --segment-color SEGMENT_COLOR
-
Plot segment lines in this color. Value can be any string accepted by matplotlib, e.g. 'red' or '#CC0000'.
- --title TITLE
-
Plot title. [Default: sample ID, from filename or -i]
- -t, --trend
-
Draw a smoothed local trendline on the scatter plot.
- --y-max Y_MAX
-
y-axis upper limit.
- --y-min Y_MIN
-
y-axis lower limit.
- --fig-size WIDTH HEIGHT
-
Width and height of the plot in inches. [Default: Predefined in Matplotlib 'rcParams' variable (most of the time: '6.4 4.8')]
To plot SNP b-allele frequencies:
- -v FILENAME, --vcf FILENAME
-
VCF file name containing variants to plot for SNV b-allele frequencies.
- -i SAMPLE_ID, --sample-id SAMPLE_ID
-
Name of the sample in the VCF to use for b-allele frequency extraction and as the default plot title.
- -n NORMAL_ID, --normal-id NORMAL_ID
-
Corresponding normal sample ID in the input VCF. This sample is used to select only germline SNVs to plot.
- -m MIN_VARIANT_DEPTH, --min-variant-depth MIN_VARIANT_DEPTH
-
Minimum read depth for a SNV to be used in the b-allele frequency calculation. [Default: 20]
- -z [ALT_FREQ], --zygosity-freq [ALT_FREQ]
-
Ignore VCF's genotypes (GT field) and instead infer zygosity from allele frequencies. [Default if used without a number: 0.25]