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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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KM HGG panel #1352

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

Closes #1335

This PR creates the Kaplan-Meier plot from the HGG molecular subtypes survival analysis.

But, based on previous discussion (having some trouble finding the comment where this was mentioned, @jharenza?), given the additional survival plots that have been made, it's not clear whether this should still go into Figure 4. The output directory in the code therefore should be determined as part of review discussion here.

For now, the main reviews I'm looking for are overall plot aesthetics and any feedback on the code itself.

jharenza commented 2 years ago

@sjspielman thanks for working on this! Can you double check your legend because it looks like the colors aren't assigned to the correct subgroups based on survival. Otherwise, aesthetics look nice and yes I think adding to figure 4 still makes sense.

sjspielman commented 2 years ago

Can you double check your legend because it looks like the colors aren't assigned to the correct subgroups based on survival

Good catch! I had tried to change the levels so the legend order matched the line order, but I guess that didn't work..

I'll try to make it work, and if I can't the legend order will somewhat differ from the line order (which isn't a big deal I think), and I'll send it into Fig 4.

jharenza commented 2 years ago

the legend order will somewhat differ from the line order (which isn't a big deal I think)

yeah nbd! :P

sjspielman commented 2 years ago

@jharenza ready for another look!

@jaclyn-taroni I included the format() function but had to do some calcs to get there. The model itself doesn't contain the P-value (ggsurvplot() calculates it under the hood).

sjspielman commented 2 years ago

Does not require CI so merging before checks complete.