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HelenaLC / CATALYST

Cytometry dATa anALYsis Tools
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How to identify/visualize co-expression (correlation) between markers? #379

Closed WilliamMWei closed 6 months ago

WilliamMWei commented 7 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.

HelenaLC commented 6 months ago

Two things come to mind: 1) this is nothing CATALYST-related per se, but can be done using basic R infrastructure, e.g., pulling out the expression matrix and using a plotting library of your choice such as ggplot2; 2) CATALYST does have the plotScatter() function to visualize biscatter plots of expression, optionally coloring cells by metadata of interest; however, for more customized/specialized plots I'd recommend option 1).