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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Update Table 1 to use broad_histology_display #1554

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

Closes #1553

This PR updates Table 1 to use broad_histology_display for the heading. I updated the table notebook to read in and incorporate the palette file and re-ran the notebook. The output column now says "broad_histology_display" which I think is appropriate because the values indeed differ from "broad_histology."

Something else I am realizing is that we may need to update Table S1 also (the histologies file), OR include docs for how to map "internal naming" back to the naming used in the manuscript, for when broad_histology != broad_histology_display. If we want to consider doing that I can add that into this PR.

jashapiro commented 2 years ago

Something else I am realizing is that we may need to update Table S1 also (the histologies file), OR include docs for how to map "internal naming" back to the naming used in the manuscript, for when broad_histology != broad_histology_display. If we want to consider doing that I can add that into this PR.

I think we should probably leave S1 as is, but I agree about adding in documentation about the groups. If Table S1 is the only place that we use the broad_histology values, we might note it in the caption for that table.

jharenza commented 2 years ago

Something else I am realizing is that we may need to update Table S1 also (the histologies file), OR include docs for how to map "internal naming" back to the naming used in the manuscript, for when broad_histology != broad_histology_display. If we want to consider doing that I can add that into this PR.

I think we should probably leave S1 as is, but I agree about adding in documentation about the groups. If Table S1 is the only place that we use the broad_histology values, we might note it in the caption for that table.

We can also possibly link to the palette file somewhere in the STAR methods?