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Merge c26f47e into a5fd3da
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@zhewa
zhewa committed Oct 7, 2020
2 parents a5fd3da + c26f47e commit d39270f
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Showing 6 changed files with 116 additions and 134 deletions.
76 changes: 38 additions & 38 deletions R/factorizeMatrix.R
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Original file line number Diff line number Diff line change
Expand Up @@ -108,15 +108,15 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_CG"),
nGByTS <- p$nGByTS
nGByTS[nGByTS == 0] <- 1

nGByTS <- matrix(0, nrow = length(y), ncol = L)
nGByTS[cbind(seq(nG), y)] <- p$nByG
GByTS <- matrix(0, nrow = length(y), ncol = L)
GByTS[cbind(seq(nG), y)] <- p$nByG

LNames <- paste0("L", seq(L))
KNames <- paste0("K", seq(K))
colnames(nTSByC) <- matrixNames(celdaMod)$column
rownames(nTSByC) <- LNames
colnames(nGByTS) <- LNames
rownames(nGByTS) <- matrixNames(celdaMod)$row
colnames(GByTS) <- LNames
rownames(GByTS) <- matrixNames(celdaMod)$row
rownames(mCPByS) <- KNames
colnames(mCPByS) <- matrixNames(celdaMod)$sample
colnames(nTSByCP) <- KNames
Expand All @@ -132,7 +132,7 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_CG"),
sample = mCPByS,
cellPopulation = nTSByCP,
cell = nTSByC,
module = nGByTS,
module = GByTS,
geneDistribution = nGByTS
)
res <- c(res, list(counts = countsList))
Expand All @@ -147,8 +147,8 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_CG"),
)

uniqueY <- sort(unique(y))
tempNGByTS <- nGByTS
tempNGByTS[, uniqueY] <- normalizeCounts(tempNGByTS[, uniqueY],
tempGByTS <- GByTS
tempGByTS[, uniqueY] <- normalizeCounts(tempGByTS[, uniqueY],
normalize = "proportion"
)
tempNGByTS <- nGByTS / sum(nGByTS)
Expand All @@ -159,14 +159,14 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_CG"),
),
cellPopulation = tempNTSByCP,
cell = normalizeCounts(nTSByC, normalize = "proportion"),
module = tempNGByTS,
module = tempGByTS,
geneDistribution = tempNGByTS
)
res <- c(res, list(proportions = propList))
}

if (any("posterior" %in% type)) {
gs <- nGByTS
gs <- GByTS
gs[cbind(seq(nG), y)] <- gs[cbind(seq(nG), y)] + delta
gs <- normalizeCounts(gs, normalize = "proportion")
tempNGByTS <- (nGByTS + gamma) / sum(nGByTS + gamma)
Expand Down Expand Up @@ -299,19 +299,19 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_G"),
nByG <- p$nByG
nByTS <- p$nByTS
nGByTS <- p$nGByTS
nGByTS[nGByTS == 0] <- 1
nM <- p$nM
nG <- p$nG
rm(p)

nGByTS[nGByTS == 0] <- 1
nGByTS <- matrix(0, nrow = length(y), ncol = L)
nGByTS[cbind(seq(nG), y)] <- nByG
GByTS <- matrix(0, nrow = length(y), ncol = L)
GByTS[cbind(seq(nG), y)] <- nByG

LNames <- paste0("L", seq(L))
colnames(nTSByC) <- matrixNames(celdaMod)$column
rownames(nTSByC) <- LNames
colnames(nGByTS) <- LNames
rownames(nGByTS) <- matrixNames(celdaMod)$row
colnames(GByTS) <- LNames
rownames(GByTS) <- matrixNames(celdaMod)$row
names(nGByTS) <- LNames

countsList <- c()
Expand All @@ -322,7 +322,7 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_G"),
if (any("counts" %in% type)) {
countsList <- list(
cell = nTSByC,
module = nGByTS,
module = GByTS,
geneDistribution = nGByTS
)
res <- c(res, list(counts = countsList))
Expand All @@ -331,8 +331,8 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_G"),
if (any("proportion" %in% type)) {
## Need to avoid normalizing cell/gene states with zero cells/genes
uniqueY <- sort(unique(y))
tempNGByTS <- nGByTS
tempNGByTS[, uniqueY] <- normalizeCounts(tempNGByTS[, uniqueY],
tempGByTS <- GByTS
tempGByTS[, uniqueY] <- normalizeCounts(tempGByTS[, uniqueY],
normalize = "proportion"
)
tempNGByTS <- nGByTS / sum(nGByTS)
Expand All @@ -341,14 +341,14 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_G"),
cell = normalizeCounts(nTSByC,
normalize = "proportion"
),
module = tempNGByTS,
module = tempGByTS,
geneDistribution = tempNGByTS
)
res <- c(res, list(proportions = propList))
}

if (any("posterior" %in% type)) {
gs <- nGByTS
gs <- GByTS
gs[cbind(seq(nG), y)] <- gs[cbind(seq(nG), y)] + delta
gs <- normalizeCounts(gs, normalize = "proportion")
tempNGByTS <- (nGByTS + gamma) / sum(nGByTS + gamma)
Expand Down Expand Up @@ -454,15 +454,15 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_G"),
nGByTS <- p$nGByTS
nGByTS[nGByTS == 0] <- 1

nGByTS <- matrix(0, nrow = length(y), ncol = L)
nGByTS[cbind(seq(nG), y)] <- p$nByG
GByTS <- matrix(0, nrow = length(y), ncol = L)
GByTS[cbind(seq(nG), y)] <- p$nByG

LNames <- paste0("L", seq(L))
KNames <- paste0("K", seq(K))
colnames(nTSByC) <- colnames(sce)
rownames(nTSByC) <- LNames
colnames(nGByTS) <- LNames
rownames(nGByTS) <- rownames(sce)
colnames(GByTS) <- LNames
rownames(GByTS) <- rownames(sce)
rownames(mCPByS) <- KNames
colnames(mCPByS) <- S4Vectors::metadata(sce)$celda_parameters$sampleLevels
colnames(nTSByCP) <- KNames
Expand All @@ -478,7 +478,7 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_G"),
sample = mCPByS,
cellPopulation = nTSByCP,
cell = nTSByC,
module = nGByTS,
module = GByTS,
geneDistribution = nGByTS
)
res <- c(res, list(counts = countsList))
Expand All @@ -493,8 +493,8 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_G"),
)

uniqueY <- sort(unique(y))
tempNGByTS <- nGByTS
tempNGByTS[, uniqueY] <- normalizeCounts(tempNGByTS[, uniqueY],
tempGByTS <- GByTS
tempGByTS[, uniqueY] <- normalizeCounts(tempGByTS[, uniqueY],
normalize = "proportion"
)
tempNGByTS <- nGByTS / sum(nGByTS)
Expand All @@ -503,14 +503,14 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_G"),
sample = normalizeCounts(mCPByS, normalize = "proportion"),
cellPopulation = tempNTSByCP,
cell = normalizeCounts(nTSByC, normalize = "proportion"),
module = tempNGByTS,
module = tempGByTS,
geneDistribution = tempNGByTS
)
res <- c(res, list(proportions = propList))
}

if (any("posterior" %in% type)) {
gs <- nGByTS
gs <- GByTS
gs[cbind(seq(nG), y)] <- gs[cbind(seq(nG), y)] + delta
gs <- normalizeCounts(gs, normalize = "proportion")
tempNGByTS <- (nGByTS + gamma) / sum(nGByTS + gamma)
Expand Down Expand Up @@ -548,19 +548,19 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_G"),
nByG <- p$nByG
nByTS <- p$nByTS
nGByTS <- p$nGByTS
nGByTS[nGByTS == 0] <- 1
nM <- p$nM
nG <- p$nG
rm(p)

nGByTS[nGByTS == 0] <- 1
nGByTS <- matrix(0, nrow = length(y), ncol = L)
nGByTS[cbind(seq(nG), y)] <- nByG
GByTS <- matrix(0, nrow = length(y), ncol = L)
GByTS[cbind(seq(nG), y)] <- nByG

LNames <- paste0("L", seq(L))
colnames(nTSByC) <- colnames(sce)
rownames(nTSByC) <- LNames
colnames(nGByTS) <- LNames
rownames(nGByTS) <- rownames(sce)
colnames(GByTS) <- LNames
rownames(GByTS) <- rownames(sce)
names(nGByTS) <- LNames

countsList <- c()
Expand All @@ -571,7 +571,7 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_G"),
if (any("counts" %in% type)) {
countsList <- list(
cell = nTSByC,
module = nGByTS,
module = GByTS,
geneDistribution = nGByTS
)
res <- c(res, list(counts = countsList))
Expand All @@ -580,8 +580,8 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_G"),
if (any("proportion" %in% type)) {
## Need to avoid normalizing cell/gene states with zero cells/genes
uniqueY <- sort(unique(y))
tempNGByTS <- nGByTS
tempNGByTS[, uniqueY] <- normalizeCounts(tempNGByTS[, uniqueY],
tempGByTS <- GByTS
tempGByTS[, uniqueY] <- normalizeCounts(tempGByTS[, uniqueY],
normalize = "proportion"
)
tempNGByTS <- nGByTS / sum(nGByTS)
Expand All @@ -590,14 +590,14 @@ setMethod("factorizeMatrix", signature(x = "matrix", celdaMod = "celda_G"),
cell = normalizeCounts(nTSByC,
normalize = "proportion"
),
module = tempNGByTS,
module = tempGByTS,
geneDistribution = tempNGByTS
)
res <- c(res, list(proportions = propList))
}

if (any("posterior" %in% type)) {
gs <- nGByTS
gs <- GByTS
gs[cbind(seq(nG), y)] <- gs[cbind(seq(nG), y)] + delta
gs <- normalizeCounts(gs, normalize = "proportion")
tempNGByTS <- (nGByTS + gamma) / sum(nGByTS + gamma)
Expand Down

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