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mbhall88 / head_to_head_pipeline

Snakemake pipelines to run the analysis for the Illumina vs. Nanopore comparison.
GNU General Public License v3.0
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Visualise available phenotype information #78

Closed mbhall88 closed 3 years ago

mbhall88 commented 3 years ago

One (potential) figure for the paper is - quoting Zam

We have samples from Madagascar, S Africa, Birmingham with illumina+ont data, plus a heterogeneous collection of phenotype data. Maybe simplest to summarise with an upset plot? Rows=country, columns = Rif+inh+emb culture phenotypes, strep pheno, amikacin pheno,…LPA for drug X,….

I am going to tentatively say ignore country as it adds on categorical variable too many and confuses things.

I am going to dump a few examples here and we can iterate

These examples show samples that have passed QC only

mbhall88 commented 3 years ago

This is with all drugs in their own category, and with LPA data also (those with -LPA suffix)

image

mbhall88 commented 3 years ago

This is the same as above, with the LPA data removed - so only culture-based DST

image

mbhall88 commented 3 years ago

@iqbal-lab feel free to reel off any other variations/changes you can think of