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scrublet-python.txt
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%matplotlib inline
import scrublet as scr
import scipy.io
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import os
os.chdir("/sdb/jxx/MTR")
os.getcwd()
counts_matrix=pd.read_csv('V3E7.csv', header=0,index_col=0).T
scrub = scr.Scrublet(counts_matrix, expected_doublet_rate=0.048)
doublet_scores, predicted_doublets = scrub.scrub_doublets(min_counts=2, min_cells=3, min_gene_variability_pctl=85, n_prin_comps=30)
scrub.plot_histogram()
predicted_doublets=scrub.call_doublets(threshold=0.12)
scrub.plot_histogram()
doub = { 'doublet_s': scrub.predicted_doublets_,
'score_s': scrub.doublet_scores_obs_ }
doub=pd.DataFrame(doub)
np.savetxt('V3E7-scrublet.csv', doub, delimiter = ',')
counts_matrix=pd.read_csv('V3E8.csv', header=0,index_col=0).T
scrub = scr.Scrublet(counts_matrix, expected_doublet_rate=0.049)
doublet_scores, predicted_doublets = scrub.scrub_doublets(min_counts=2, min_cells=3, min_gene_variability_pctl=85, n_prin_comps=30)
scrub.plot_histogram()
predicted_doublets=scrub.call_doublets(threshold=0.10)
scrub.plot_histogram()
doub = { 'doublet_s': scrub.predicted_doublets_,
'score_s': scrub.doublet_scores_obs_ }
doub=pd.DataFrame(doub)
np.savetxt('V3E8-scrublet.csv', doub, delimiter = ',')
counts_matrix=pd.read_csv('V3E9.csv', header=0,index_col=0).T
scrub = scr.Scrublet(counts_matrix, expected_doublet_rate=0.069)
doublet_scores, predicted_doublets = scrub.scrub_doublets(min_counts=2, min_cells=3, min_gene_variability_pctl=85, n_prin_comps=30)
scrub.plot_histogram()
predicted_doublets=scrub.call_doublets(threshold=0.12)
scrub.plot_histogram()
doub = { 'doublet_s': scrub.predicted_doublets_,
'score_s': scrub.doublet_scores_obs_ }
doub=pd.DataFrame(doub)
np.savetxt('V3E9-scrublet.csv', doub, delimiter = ',')
counts_matrix=pd.read_csv('V3E11.csv', header=0,index_col=0).T
scrub = scr.Scrublet(counts_matrix, expected_doublet_rate=0.051)
doublet_scores, predicted_doublets = scrub.scrub_doublets(min_counts=2, min_cells=3, min_gene_variability_pctl=85, n_prin_comps=30)
scrub.plot_histogram()
predicted_doublets=scrub.call_doublets(threshold=0.10)
scrub.plot_histogram()
doub = { 'doublet_s': scrub.predicted_doublets_,
'score_s': scrub.doublet_scores_obs_ }
doub=pd.DataFrame(doub)
np.savetxt('V3E11-scrublet.csv', doub, delimiter = ',')
counts_matrix=pd.read_csv('V3E13.csv', header=0,index_col=0).T
scrub = scr.Scrublet(counts_matrix, expected_doublet_rate=0.053)
doublet_scores, predicted_doublets = scrub.scrub_doublets(min_counts=2, min_cells=3, min_gene_variability_pctl=85, n_prin_comps=30)
scrub.plot_histogram()
predicted_doublets=scrub.call_doublets(threshold=0.10)
scrub.plot_histogram()
doub = { 'doublet_s': scrub.predicted_doublets_,
'score_s': scrub.doublet_scores_obs_ }
doub=pd.DataFrame(doub)
np.savetxt('V3E13-scrublet.csv', doub, delimiter = ',')