Closed patrickjdanaher closed 2 years ago
Note that this approach could also allow for incorporation of immunofluorescence info.
Basic approach:
Function 1: "fastNeighborhoodFactorization":
Function 2: "fastCohorting"
Function 3: "update_logliks_with_cohort_freqs"
Implemented in the iss132-cohorting branch. Not yet merged.
merged
Spatial context has information to offer cell typing. (Though often it's better to ignore this information if downstream you'll be running DE vs. spatial variables.)
Proposal to incorporate spatial information:
Even better, average the cluster freqs with the base rates.Or add 1000 cells' worth of counts from the baseline frequencies.The impact of the above will be modest. It won't reshape the whole cell typing outcome, but it will act as a tiebreaker for more ambiguous cells.