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Sage-Bionetworks / NF_LandscapePaper_2019

This repository hosts all the code used to generate analyses and figures for the landscape paper
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adding immune - lv correlations #15

Closed allaway closed 4 years ago

allaway commented 4 years ago

This analysis correlates multiPLIER latent variables with cibersort/immune scores. The code is largely the same as notebook 03.

There are several LVs that seem to correlate pretty well with immune cell types. Unsurprisingly, most of these are immune latent variables! This makes for a nice internal control. There are several LVs that are not explicitly listed as immune pathways/cell types, but they still very well could be...

One change from notebook 03 was to look for absolute correlation when plotting, so we also get negatively correlated things (< -0.6 correlation).

I also switched to using Spearman correlation since the data do not appear to be normally distributed.

Finally, i think we'd get better correlations if we did this evaluation by tumor type, rather than calculating correlation across all samples, as the different tumor types seem to have different lv-immune cell correlations from one another (looking at the plots,anyway).

allaway commented 4 years ago

https://htmlpreview.github.io/?https://raw.githubusercontent.com/Sage-Bionetworks/NF_LandscapePaper_2019/8596f99a7fb7792df0c757c5c34565a9ec0ffcbe/results/07-ImmuneDeconv-LatentVariableCorrelation.html?token=AE3WNSADT25AOZXVO65RYW25VDLRC

allaway commented 4 years ago

Closes #9