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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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area analysis on DATA.TABLE #111

Open Mark-Ste opened 2 years ago

Mark-Ste commented 2 years ago

Hi, We encountered an error trying out the adv spatial 3 workflow. During 'area analysis on the DATA. TABLE' the processing of a ROI stopped with

Processing ROI002 -- (2 / 12) -- Calculating distribution -- Calculating composition -- Calculating cell counts -- Calculating counts/area -- Calculating distance and adjacency Region: A Error in gtools::permutations(n = length(reg.pops), r = 2, v = reg.pops, : bad value of n

In ROI002 no cells are annotated with region A, so this might cause the problem. Is there a way to overcome this and continue analysis without removing ROI002 from the analysis?

Thanks and great work! Markus

tomashhurst commented 2 years ago

Hi Markus,

We are actually working on a fix for this issue at the moment, so we will get back to you soon!

In the meantime, you have the option of removing that particular ROI -- and running a separate spatial analysis on it.

Tom