New figure code

additional_benchmarks/Snakefile

@@ -101,5 +101,28 @@ rule combine:
  combined_df = pd.concat(dfs, ignore_index=True)
  combined_df.to_csv(output[0], sep="\t", index=False)
 
-rule merge:
+rule figure:
  input: "combined_benchmarks.tsv"
+ output: "benchmark_figure.pdf"
+ run:
+ import matplotlib.pyplot as plt
+ import matplotlib as mpl
+ mpl.use('agg')
+ import pandas as pd
+ d = pd.read_csv(input[0], sep="\t")
+ d = d.groupby(['tool', 'size'], as_index=False)['s'].median()
+ fig, ax = plt.subplots()
+ for tool in d['tool'].unique():
+ data = d[d['tool'] == tool]
+ ax.plot(data['size'], data['s'], '-o', label=tool)
+ ax.set_title('Benchmark Results')
+ ax.semilogx()
+ ax.semilogy()
+ ax.set_xlabel('Number of BED ranges')
+ ax.set_ylabel('Time (s)')
+ ax.legend()
+ plt.tight_layout()
+ plt.savefig('benchmark_figure.pdf')
+
+rule merge:
+ input: "benchmark_figure.pdf"