add benchmark source code for reproducibility

Author: frankligy

reproduce/final_submission_2022/scalability/benchmark.py

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+#! /data/salomonis2/LabFiles/Frank-Li/citeseq/scanpy_new_env/bin/python3.6
+
+import pandas as pd
+import numpy as np
+import os,sys
+import scanpy as sc
+import matplotlib.pyplot as plt
+import matplotlib as mpl
+
+mpl.rcParams['pdf.fonttype'] = 42
+mpl.rcParams['ps.fonttype'] = 42
+mpl.rcParams['font.family'] = 'Arial'
+
+# plot for effects on annotations
+
+n_anno = [3,6,9,12]
+time_run = [389,497,639,2090]
+time_cpu = [1061,2511,6511,40515]
+
+fig,ax = plt.subplots()
+ax.plot(np.arange(len(n_anno)),[item/60 for item in time_run],linestyle='--',marker='o',label='run time')
+ax.plot(np.arange(len(n_anno)),[item/60 for item in time_cpu],linestyle='--',marker='o',label='cpu time')
+ax.set_xticks(np.arange(len(n_anno)))
+ax.set_xticklabels(n_anno)
+ax.set_xlabel('# annotations')
+ax.set_ylabel('Running time (mins)')
+ax.set_title('Effects of number of annotations on Running time -- CITE')
+ax.legend(frameon=False,loc='upper left',bbox_to_anchor=(1,1))
+plt.savefig('anno.pdf',bbox_inches='tight')
+plt.close()
+
+
+# plot for effects on cells
+
+n_cells = [10000,20000,30000,40000]
+time_run = [714,1341,1991,2456]
+
+fig,ax = plt.subplots()
+ax.plot(np.arange(len(n_cells)),[item/60 for item in time_run],linestyle='--',marker='o',label='run time')
+ax.set_xticks(np.arange(len(n_cells)))
+ax.set_xticklabels(n_cells)
+ax.set_xlabel('# cells')
+ax.set_ylabel('Running time (mins)')
+ax.set_title('Effects of number of cells on Running time -- LUNG')
+ax.legend(frameon=False,loc='upper left',bbox_to_anchor=(1,1))
+plt.savefig('cells.pdf',bbox_inches='tight')
+plt.close()
+
+
+# plot for effects on 
+
+n_features = [40000,60000,80000,100000]
+time_run = [1233,1759,2547,3632]
+
+fig,ax = plt.subplots()
+ax.plot(np.arange(len(n_features)),[item/60 for item in time_run],linestyle='--',marker='o',label='run time')
+ax.set_xticks(np.arange(len(n_features)))
+ax.set_xticklabels(n_features)
+ax.set_xlabel('# features')
+ax.set_ylabel('Running time (mins)')
+ax.set_title('Effects of number of features on Running time -- MULTIOME')
+ax.legend(frameon=False,loc='upper left',bbox_to_anchor=(1,1))
+plt.savefig('features.pdf',bbox_inches='tight')
+plt.close()
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