accuracy/sensitivity figures

deconvolution/main/fig_gen.py

+import argparse
+import pandas as pd
+import plotnine as p9
+
+
+def parse_args():
+    parser = argparse.ArgumentParser(description='Take an input tsv with Acc/Sens values and generate figs')
+    parser.add_argument('filename', type=str,
+                        help='The tsv file')
+    parser.add_argument('--output', '-o', type=str, default='', help="The output file prefix. Default prefix is <input>")
+
+    args = parser.parse_args()
+
+    if args.output == "":
+        args.output = ".".join(args.filename.split(".")[:-1])
+
+    return args
+
+
+def main():
+    args = parse_args()
+    data = pd.read_csv(args.filename, sep='\t')
+    print(data)
+    plot = (p9.ggplot(data=data,
+                     mapping=p9.aes(x='path length', y='Accuracy', color='experiment'))
+            + p9.geom_line())
+    plot.save(args.output + "_acc.png", width=10, height=3, dpi=300)
+
+    plot = (p9.ggplot(data=data,
+                     mapping=p9.aes(x='path length', y='Sensitivity', color='experiment'))
+            + p9.geom_line())
+    plot.save(args.output + "_sens.png", width=10, height=3, dpi=300)
+
+
+
+if __name__ == "__main__":
+    main()

figs/fig1_data.tsv

+experiment	path length	Accuracy	Sensitivity
+5000-2-0 Gb	2	0.48	1.0
+5000-2-0 Gb	4	0.09	1.0
+5000-2-0 Gb	10	0	0.99
+5000-2-0 Gb	100	0	0.94
+5000-2-0 lcp	2	1.0	1.0
+5000-2-0 lcp	4	1.0	0.99
+5000-2-0 lcp	10	1.0	0.98
+5000-2-0 lcp	100	1.0	0.88
+5000-2-1 Gb	2	0.46	1.0
+5000-2-1 Gb	4	0.09	1.0
+5000-2-1 Gb	10	0	1.0
+5000-2-1 Gb	100	0	0.98
+5000-2-1 lcp	2	1	1
+5000-2-1 lcp	4	1	0.99
+5000-2-1 lcp	10	1	0.98
+5000-2-1 lcp	100	0.99	0.84
+5000-3-0 Gb	2	0.31	1
+5000-3-0 Gb	4	0.03	1
+5000-3-0 Gb	10	0	0.99
+5000-3-0 Gb	100	0	0.88
+5000-3-0 lcp	2	1	0.99
+5000-3-0 lcp	4	1	0.98
+5000-3-0 lcp	10	0.99	0.95
+5000-3-0 lcp	100	0.99	0.6
+5000-3-1 Gb	2	0.33	1
+5000-3-1 Gb	4	0.03	1
+5000-3-1 Gb	10	0	1
+5000-3-1 Gb	100	0	0.96
+5000-3-1 lcp	2	1	0.99
+5000-3-1 lcp	4	1	0.97
+5000-3-1 lcp	10	0.99	0.93
+5000-3-1 lcp	100	0.95	0.54
\ No newline at end of file

requirements.txt

@@ -6,3 +6,6 @@ scipy
 numpy
 python-louvain
 intervaltree
+
+pandas
+ggplot