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Parent: Release 1.0.2
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Dev project bulk atac2 #1390

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d5ed45d
make .safeSubset flexible to matrix and dgCMatrix input
rcorces Apr 15, 2022
3663b50
force a matrix to be passed to safeSubset
rcorces Apr 15, 2022
a7abaa4
params must be a list, not a vector
rcorces Apr 15, 2022
9db334e
fix logic of dimsToUse in projectBulkATAC
rcorces Apr 15, 2022
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10 changes: 5 additions & 5 deletions R/BulkProjection.R
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ projectBulkATAC <- function(
# Create Bulk Matrix
##################################################
bulkMat <- .safeSubset(
mat = .getAssay(subATAC, "counts"),
mat = as.matrix(.getAssay(subATAC, "counts")),
subsetRows = paste0("f", seq_along(rDGR))
)
.logThis(bulkMat, "bulkATACMat", logFile = logFile)
Expand Down Expand Up @@ -145,13 +145,15 @@ projectBulkATAC <- function(
if(!is.null(corCutOff)){
if(scaleDims){
corToDepth <- rD$corToDepth$scaled
dimsToUse <- dimsToUse[corToDepth < corCutOff]
dimsToUse <- dimsToUse[intersect(dimsToUse, which(corToDepth < corCutOff))]
}else{
corToDepth <- rD$corToDepth$none
dimsToUse <- dimsToUse[corToDepth < corCutOff]
dimsToUse <- dimsToUse[intersect(dimsToUse, which(corToDepth < corCutOff))]
}
}

simRD <- simRD[, dimsToUse, drop = FALSE]

if(embedding$params$nc != ncol(simRD)){
.logMessage("Error! Inconsistency found with matching LSI dimensions to those used in addUMAP or addTSNE",
"\nReturning with simulated reduced dimension coordinates...", verbose = TRUE, logFile = logFile)
Expand All @@ -161,8 +163,6 @@ projectBulkATAC <- function(
return(out)
}

simRD <- simRD[, dimsToUse, drop = FALSE]

}

##################################################
Expand Down
4 changes: 2 additions & 2 deletions R/Embedding.R
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Original file line number Diff line number Diff line change
Expand Up @@ -170,7 +170,7 @@ addUMAP <- function(

ArchRProj@embeddings[[name]] <- SimpleList(
df = dfEmbedding,
params = c(
params = list(
embeddingParams,
dimsToUse = dimsToUse,
scaleDims = scaleDims,
Expand All @@ -189,7 +189,7 @@ addUMAP <- function(
embeddingParams$X <- NULL
ArchRProj@embeddings[[name]] <- SimpleList(
df = dfEmbedding,
params = c(
params = list(
embeddingParams,
dimsToUse = dimsToUse,
scaleDims = scaleDims,
Expand Down
23 changes: 21 additions & 2 deletions R/HiddenUtils.R
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Original file line number Diff line number Diff line change
Expand Up @@ -188,8 +188,18 @@
idxNotIn <- which(subsetRows %ni% rownames(mat))
if(length(idxNotIn) > 0){
subsetNamesNotIn <- subsetRows[idxNotIn]
matNotIn <- Matrix::sparseMatrix(i=1,j=1,x=0,dims=c(length(idxNotIn), ncol = ncol(mat)))

#check matrix class and make a matching empty matrix for the idxNotIn rows
if (class(mat)[[1]] == "dgCMatrix") {
matNotIn <- Matrix::sparseMatrix(i = 1, j = 1, x = 0, dims = c(length(idxNotIn), ncol = ncol(mat)))
} else if (class(mat)[[1]] == "matrix") {
matNotIn <- matrix(nrow = length(idxNotIn), ncol = ncol(mat), 0)
} else{
stop("Error! Argument 'mat' in .safeSubset is not either of class matrix or class dgCMatrix!")
}

rownames(matNotIn) <- subsetNamesNotIn
colnames(matNotIn) <- colnames(mat)
mat <- rbind(mat, matNotIn)
}
mat <- mat[subsetRows,]
Expand All @@ -199,7 +209,16 @@
idxNotIn <- which(subsetCols %ni% colnames(mat))
if(length(idxNotIn) > 0){
subsetNamesNotIn <- subsetCols[idxNotIn]
matNotIn <- Matrix::sparseMatrix(i=1,j=1,x=0,dims=c(nrow(mat), ncol = length(idxNotIn)))

#check matrix class and make a matching empty matrix for the idxNotIn rows
if (class(mat)[[1]] == "dgCMatrix") {
matNotIn <- Matrix::sparseMatrix(i = 1, j = 1, x = 0, dims = c(nrow(mat), ncol = length(idxNotIn)))
} else if (class(mat)[[1]] == "matrix") {
matNotIn <- matrix(nrow = nrow(mat), ncol = length(idxNotIn), 0)
} else{
stop("Error! Argument 'mat' in .safeSubset is not either of class matrix or class dgCMatrix!")
}
rownames(matNotIn) <- rownames(mat)
colnames(matNotIn) <- subsetNamesNotIn
mat <- cbind(mat, matNotIn)
}
Expand Down