mixcr overlapScatterPlot

mixcr overlapScatterPlot creates a scatter-plot for clone frequencies overlap between two samples.

Command line options

mixcr overlapScatterPlot --downsampling (<type>|none) [--chains <chain>[,<chain>...]]... [--only-productive] [--criteria <s>] [--method <method>] [--no-log] [--force-overwrite] [--no-warnings] [--verbose] [--help] cloneset_1.(clns|clna) cloneset_2.(clns|clna) output.(pdf|eps|svg|png|jpeg)

The command takes .clna or .clns file as input and produces one of the following graphical formats depending on the extension of output file: .pdf, .eps, .png, .svg and .jpeg

--downsampling (<type>|none)

Choose downsampling applied to normalize the clonesets. Possible values: count-[reads|TAG]-[auto|min|fixed][-<number>], top-[reads|TAG]-[<number>], cumtop-[reads|TAG]-[percent], none

--chains <chain>[,<chain>...]

Chains to export.

--only-productive

Filter out-of-frame sequences and sequences with stop-codons.

--criteria <s>

Overlap criteria. Defines the rules to treat clones as equal. Default: CDR3|AA|V|J (For two clones to me equal they must share CDR3 amino acid sequence, V and J genes)

--method <method>

Correlation method to use. Possible value: Pearson, Kendall, Spearman. Default: Pearson

--no-log

Do not apply log10 to clonotype frequencies.

-f, --force-overwrite

Force overwrite of output file(s).

-nw, --no-warnings

Suppress all warning messages.

--verbose

Verbose messages.

-h, --help

Show this help message and exit.

Example:

```shell

mixcr overlapScatterPlot \ --downsampling none \ --chains IGH \ results/M1_4T1_Blood_S2.clns results/M1_4T1_Blood_S6.clns \ M1_4T1_Blood.overlap.pdf ```