Cytomap Cell Distance Tables

Been digging in to all the great functions Cytomap can offer.
Quick question, for cell-cell distance calculations, is there a plot option for mean distance or a violin plot of distances calculated from one cell type to every other? Similar to the one’s in the Cytomap paper? The only way I can tell to access the data is to plot each individual cell class and then export a csv of the calculated distance. Hoping there’s a more robust way to do this. Thanks!

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Thanks for checking out CytoMAP!

There are a few ways to deal with the distance data. For the paper I used File -> Export Data For Prism then made the violin plots in Prism because it was easiest to share those plots with my co-authors. With this export option you can export multiple cell types, multiple channels and multiple samples all at once. This does make an individual .csv file per sample so if you are trying to combine many samples into one violing plot it can be a bit tedious.

You can also make violin plots directly in CytoMAP using the Bar and Violin Plots Extension. Here you can either make bar graphs of the mean channel values or violin plots of the raw channel values. You can also normalize the data. I am still working on getting data to correctly export from these violin plots so if you want to export this data use the Export Data For Prism option in the main CytoMAP window.

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Thanks for the quick reply. Didn’t notice those extensions! Working great.

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