added function to easily plot signatures from exposures signatures an… #3
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mdml
requested changes
Dec 19, 2018
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Code looks fine but we should clean up before merging:
- Describe contributions and testing in pull request. Also include an example output plot.
- The build is broken. What's going on there? Would be great to have one of these plots automatically produced by Travis as well
| # counts_df is samples-by-categories | ||
| # exposures_df samples-by-signatures | ||
| # signatures_df is signatures-by-categories | ||
| def plot_signatures(counts_df, signature_df, exposure_df, output_file): |
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Add palette and ylabel as optional arguments
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More specifically, try to make the function call match the sbs_signature_plot (since you are eventually calling tht)
| # and calculate the number of mutations attribution to signature i in sample j | ||
| contrib += exposure_df.loc[sample, sig]*counts_df.loc[sample].sum() # calculate the contribution | ||
| output.append(signature_df.loc[sig]*contrib) | ||
| #contribs[sig].append(phi[i]*contrib) |
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Not sure we need to keep commented out code around
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…d counts