Description Usage Arguments Value
View source: R/melanoma_spatial.R
Get cell counts and densities by cell definition rather than marker combination
1 | summarizeByCellTypeDefinition(assignments, bandArea, config, plotConfigFile)
|
assignments |
table of 0s and 1s, where columns are markers (may be pos or neg) and each row is a unique cell; zero indicates cell is NOT positive for that marker (note, if marker name is negative a zero means the opposite) and one indicates positivity |
bandArea |
table indicating calculated area for each sample, fov and band |
config |
parsed marker config of info for each cell type definition including marker combinations (result of getMarkerConfig()) |
plotConfigFile |
full path to file containing plot options including colors for cell types |
list of two items: den=density table, config=updated config to represent summary info
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