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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 warning messages.
-h, --help
Show this help message and exit.

Example:

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

img.png