angelolab / angelolab/publications

Missing file for Figure 3 reproduction: timepoint_combined_features_outcome_labels.csv

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Hi,

Thank you for making the TONIC data and code publicly available.

I am trying to reproduce Figure 3 using the public Zenodo release together with the GitHub code. However, the Figure 3 script references the file:

analysis_files/timepoint_combined_features_outcome_labels.csv

This file does not appear to be included in the Zenodo package I downloaded.

In analysis_files, I can find files such as:

timepoint_combined_features.csv

timepoint_evolution_features.csv

timepoint_features.csv

timepoint_features_filtered.csv

but not timepoint_combined_features_outcome_labels.csv.

From the script, it seems that this file is specifically needed for panels Fig. 3f/3g, since it contains the Clinical_benefit column used for grouping samples.
I understand that outcome labels may not be publicly released due to privacy restrictions, but I wanted to confirm whether Fig. 3f/3g are reproducible from the public package or not.

Thank you very much for your help.

Best regards

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