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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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The calculation method of gene frequency (or copy) in RGI_Heatmap #277

Closed ZYX593889540 closed 3 weeks ago

ZYX593889540 commented 2 months ago

How is the frequency or copy number of resistance genes calculated for each sample in the obtained output table, and based on which screening is made.

agmcarthur commented 3 weeks ago

Documentation found here: https://github.com/arpcard/rgi/blob/master/docs/rgi_main.rst

Currently, frequency of ARGs within samples is not supported. Yellow represents a Perfect annotation, teal represents a Strict annotation, purple represents no ARG found.

The --frequency flag will place a histogram along the top of the figure, showing how many isolates share the same resistome profile.

For example, this is a heat map from a number of isolate genomes, where I generated RGI json output for each genome. I used the flags --frequency --cluster both.

cluster_both_frequency-39

agmcarthur commented 3 weeks ago

If within a single sample, there were two copies of an ARG, it would still only show up once.