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MacanPN / single-cell-tools

https://macanpn.github.io/single-cell-tools/namespacesc-analyses.html
MIT License
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correlation_file = "pseudotime_wo_brC/spearman_correlation.csv" #3

Open cobriniklab opened 6 years ago

cobriniklab commented 6 years ago

wondering how to generate this file for use with the genes_correlated_with_pseudotime.py script

cobriniklab commented 6 years ago 
## block of code to calculate correlations
'''
correlation_method = "spearman"
correlation_733 = get_correlation_with_pseudotime(expression_table, pt733, method=correlation_method)
correlation_737 = get_correlation_with_pseudotime(expression_table, pt737, method=correlation_method)
correlation_Ctrl = get_correlation_with_pseudotime(expression_table, ptCtrl, method=correlation_method)
'''
## combine correlations into one DataFrame
'''
corr = pd.DataFrame(0, index=correlation_733.index, columns=["Ctrl","733","737"])
corr["Ctrl"] = correlation_Ctrl
corr["733"]  = correlation_733
corr["737"]  = correlation_737
corr.to_csv("pseudotime_wo_brC/"+correlation_method+"_correlation.csv", sep="\t")
'''