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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Forest plot for panel 5D #1339

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

Closes #1336

This PR adds a forest plot for 5D, but there is an important caveats if we're going to include this plot:

The Macrophage M1 immune cell category HR has an infinite estimate and upper CI. It cannot therefore be plotted, but it is significant. It's definitely >1, but we have no precision about the estimate other than "it's big." Therefore, this needs to be discussed in the caption and in the text, because it's not possible to graphically represent the full model.

Otherwise, CD274 expression and monocyte fractions are significant, though the estimate for the latter is probably imprecise due to very wide CI.

sjspielman commented 2 years ago

Does not rely on CI so merging before checks are complete.