adding plotting AMRs (#9)

* Update amr.md * add script to plot amrfinder results * plot_amrfinder * Update amr.md * Update amr.md * Update docs/amr.md Co-authored-by: C. Titus Brown <[email protected]> --------- Co-authored-by: C. Titus Brown <[email protected]>
ngs-docs · Apr 29, 2024 · 1eddf40 · 1eddf40
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diff --git a/docs/amr.md b/docs/amr.md
@@ -16,7 +16,7 @@ of the metagenome.
 
 First, install the software. Run:
 ```
-mamba create -n amrfinder -y ncbi-amrfinderplus megahit prodigal csvtk
+mamba create -n amrfinder -y ncbi-amrfinderplus megahit prodigal csvtk matplotlib seaborn pandas
 conda activate amrfinder
 ```
 
@@ -102,3 +102,11 @@ reads to it to get the abundance. This is because assembly collapses
 the abundance of the output contigs, and you have to recover it through
 other means.
 
+
+Now we can plot the abundances of the AMRs we found:
+```
+../scripts/plot_amr.py CD136.amrfinder.tsv -o CD136.amrfinder.pdf
+```
+![CD136 amrfinder](https://github.com/AnneliektH/2024-pig-paradigm-workshop/blob/main/docs/images/CD136.amrfinder.png)
+
+
diff --git a/docs/images/CD136.amrfinder.png b/docs/images/CD136.amrfinder.png
diff --git a/scripts/plot_amr.py b/scripts/plot_amr.py
@@ -0,0 +1,24 @@
+#! /usr/bin/env python
+import pandas as pd
+import matplotlib.pyplot as plt
+import seaborn as sns
+import sys
+import argparse
+
+
+def main():
+    p = argparse.ArgumentParser()
+    p.add_argument('df')
+    p.add_argument('-o', '--output-figure', required=True)
+    args = p.parse_args()
+
+    df = pd.read_csv(args.df, sep = '\t')
+    df_all = df.Class.value_counts().to_frame().reset_index()
+    figure = sns.barplot(data=df_all, x="count", y="Class", hue="Class", legend=False)
+    figure.figure.set_size_inches(15,5)
+    figure.figure.savefig(args.output_figure)
+
+
+
+if __name__ == '__main__':
+    sys.exit(main())