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ImmuneDynamics / Spectre

A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.
https://immunedynamics.github.io/spectre/
MIT License
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How to identify/visualize co-expression (correlation) between markers? #182

Open WilliamMWei opened 10 months ago

WilliamMWei commented 10 months ago

Hi, Thank you so much for the tool.

Could you give me some pointers on packages/functions to identify/visualize the co-expression (correlations) between markers or of one marker with every other markers?

Thank you so much for your help.

I have also posted in Catalyst github for query. https://github.com/HelenaLC/CATALYST/issues/379

tomashhurst commented 10 months ago

Hi @WilliamMWei , do you mean something a bit like this (images attached)? In this case we are correlating various features, but this can be used in a similar way to look at the correlation of marker expresison.

image image

From this paper: https://www.sciencedirect.com/science/article/pii/S2666379121000197?via%3Dihub#fig6

SamGG commented 10 months ago

For visualising data frames with mixed data types, look at FunkyHeatmap.

denvercal1234GitHub commented 4 months ago

Hi @tomashhurst - I wonder if you guys are planning to release updated tutorial version soon? If so, it would be awesome if we could have this exploration of correlation heatmap given the availability of already useful bits at https://immunedynamics.io/spectre/cytometry/#tutorials.

This blog post is for sc/bulk RNAseq gene correlation/co-expression analysis, but could be adaptable? https://divingintogeneticsandgenomics.rbind.io/post/how-to-do-gene-correlation-for-single-cell-rnaseq-data-part-1/

ghar1821 commented 4 months ago

I don't think we have any functions that can do correlation/co-expression analysis. We will need to look into this.

In the meantime, I just realised that we actually have implemented a function that can create a plot similar to the one below some time ago (https://github.com/ImmuneDynamics/Spectre/blob/development/R/make.bubble.plot.R). I think I used it once for something but somehow never used it again. The plot can show correlation between different markers for each cell type, but the dot won't be showing the correlation, but rather the median marker expression. Maybe we can improve this to show the correlation values rather than median marker expression.

image image

denvercal1234GitHub commented 4 months ago

Thank you so much @ghar1821 ! Yes, it would be great to show correlation values too. Excited to see the upcoming tutorial and updates!