Reproduction of spicyR paper

[PaoloDellaPenna]

Hi, I’m having trouble reproducing the diabetes data analysis described in the article "spicyR: spatial analysis of in situ cytometry data in R". I am following the script available on GitHub, but I’m stuck at creating the correct object to pass to the spicy function because I don’t have access to the SegmentedCell function and the imagePheno function.
Could you explain what the SegmentedCell function does and how I can work around this issue?
Thank you for your time!

[ellispatrick]

Hi Paolo,

The code base for spicyR has evolved a lot since it was put on Bioconductor in 2020. SegmentedCell no longer exists, with spicyR now accepting a SingleCellExperiment or SpatialExperiment. As long as you have one of those with 1) image identifiers, 2) cell type labels and 3) x-y coordinates, then you should be good to go. You can find the vignette here... https://www.bioconductor.org/packages/release/bioc/vignettes/spicyR/inst/doc/spicyR.html

Are you specifically trying to replicate the diabetes findings? If so, it might be productive to zoom with @shreyarajeshrao who should be able to talk you through the analysis and how she interprets the findings.