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Remove legacy RIRA columns #121

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merged 1 commit into from
Aug 9, 2024
Merged

Remove legacy RIRA columns #121

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19 changes: 17 additions & 2 deletions R/CellTypist.R
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Original file line number Diff line number Diff line change
Expand Up @@ -436,7 +436,7 @@ TrainCellTypist <- function(seuratObj, labelField, modelFile, minCellsPerClass =
#'
#' @export
Classify_TNK <- function(seuratObj, assayName = Seurat::DefaultAssay(seuratObj), columnPrefix = 'RIRA_TNK_v2.', maxAllowableClasses = 6, minFractionToInclude = 0.01, minCellsToRun = 200, maxBatchSize = 600000, retainProbabilityMatrix = FALSE) {
return(RunCellTypist(seuratObj = seuratObj,
seuratObj <- RunCellTypist(seuratObj = seuratObj,
modelName = "RIRA_TNK_v2",
# These are optimized for this model:
pThreshold = 0.5, minProp = 0, useMajorityVoting = FALSE, mode = "prob_match",
Expand All @@ -448,7 +448,14 @@ Classify_TNK <- function(seuratObj, assayName = Seurat::DefaultAssay(seuratObj),
minCellsToRun = minCellsToRun,
maxBatchSize = maxBatchSize,
retainProbabilityMatrix = retainProbabilityMatrix
))
)

# Limit the resulting calls to just RIRA T/NK cells:
if ('RIRA_Immune_v2.majority_voting' %in% names([email protected])) {
seuratObj$RIRA_TNK_v2.cellclass[seuratObj$RIRA_Immune_v2.majority_voting != 'T_NK'] <- 'Other'
}

return(seuratObj)
}


Expand Down Expand Up @@ -510,6 +517,14 @@ Classify_Myeloid <- function(seuratObj, assayName = Seurat::DefaultAssay(seuratO
#'
#' @export
Classify_ImmuneCells <- function(seuratObj, assayName = Seurat::DefaultAssay(seuratObj), columnPrefix = 'RIRA_Immune_v2.', maxAllowableClasses = 6, minFractionToInclude = 0.01, minCellsToRun = 200, maxBatchSize = 600000, retainProbabilityMatrix = FALSE, filterDisallowedClasses = TRUE) {
if ('RIRA_Immune_v1.cellclass' %in% names([email protected])) {
print('Dropping legacy RIRA_Immune_v1 columns')
toDrop <- grep(names([email protected]), pattern = 'RIRA_Immune_v1', value = TRUE)
for (fn in toDrop) {
seuratObj[[fn]] <- NULL
}
}

seuratObj <- RunCellTypist(seuratObj = seuratObj,
modelName = 'RIRA_Immune_v2',

Expand Down