subset input based on labels (b1f58e00) · Commits · github_fork / DAseq2

R/SeuratMarkerFinder.R

+2 −1

Original line number	Diff line number	Diff line
		@@ -61,7 +61,8 @@ SeuratMarkerFinder <- function(
		addDAslot <- function(object, da.regions, da.slot = "da", set.ident = F){
		seurat.version <- substr(packageVersion("Seurat"),1,1)
		if(seurat.version == "3" \| seurat.version == "4"){
		object@meta.data[,da.slot] <- da.regions$da.region.label
		object@meta.data[,da.slot] <- NA
		object@meta.data[,da.slot][da.regions$cell.idx] <- da.regions$da.region.label
		if(set.ident){
		Idents(object) <- object@meta.data[,da.slot]
		}

R/getDAcells.R

+12 −1

Original line number	Diff line number	Diff line
		@@ -28,6 +28,7 @@
		#'
		#' @return a list of results
		#' \describe{
		#' \item{cell.idx}{index of cells used in DA calculation}
		#' \item{da.ratio}{score vector for each cell}
		#' \item{da.pred}{(mean) prediction from the logistic regression}
		#' \item{da.up}{index for DA cells more abundant in condition of labels.2}
		@@ -53,8 +54,15 @@ getDAcells <- function(
		!inherits(labels.1, "character") \| !inherits(labels.2, "character")){
		stop("Input parameters cell.labels, labels.1 and labels.2 must be character")
		}

		# subset input data if just using a subset of input cells
		if(length(setdiff(cell.labels, c(labels.1, labels.2))) > 0){
		stop("Input parameter cell.labels contain labels not from labels.1 or labels.2")
		warning("Input parameter cell.labels contain labels not from labels.1 or labels.2, subsetting...")
		cell.idx <- which(cell.labels %in% c(labels.1, labels.2))
		X <- X[cell.idx,]
		cell.labels <- cell.labels[cell.idx]
		} else {
		cell.idx <- seq_len(length(cell.labels))
		}
		n.cells <- length(cell.labels)

		@@ -168,6 +176,7 @@ getDAcells <- function(
		X.pred.plot <- NULL
		X.da.cells.plot <- NULL
		} else if(do.plot & !is.null(plot.embedding)){
		plot.embedding <- plot.embedding[cell.idx,]
		X.pred.plot <- plotCellScore(
		X = plot.embedding, score = X.pred, size = size
		) + theme(legend.title = element_blank())
		@@ -201,6 +210,7 @@ getDAcells <- function(
		))
		} else {
		return(list(
		cell.idx = cell.idx,
		da.ratio = X.knn.ratio,
		da.pred = X.pred,
		rand.pred = X.random.pred.list,
		@@ -306,6 +316,7 @@ updateDAcells <- function(
		X.pred.plot <- NULL
		X.da.cells.plot <- NULL
		} else if(do.plot & !is.null(plot.embedding)){
		plot.embedding <- plot.embedding[X$cell.idx,]
		X.pred.plot <- plotCellScore(
		X = plot.embedding, score = X.pred, size = size
		) + theme(legend.title = element_blank())

R/getDAregion.R

+17 −6

Original line number	Diff line number	Diff line
		@@ -24,6 +24,7 @@
		#'
		#' @return a list of results
		#' \describe{
		#' \item{cell.idx}{index of cells used in DA calculation}
		#' \item{da.region.label}{DA region label for each cell from the whole dataset,
		#' '0' represents non-DA cells.}
		#' \item{DA.stat}{a table showing DA score and p-value for each DA region}
		@@ -43,24 +44,32 @@ getDAregion <- function(
		cat("Turning X to a matrix.\n")
		X <- as.matrix(X)
		}
		n.cells <- nrow(X)
		n.dims <- ncol(X)
		if(is.null(rownames(X))){
		rownames(X) <- paste("C",c(1:n.cells), sep = "")
		}

		# check label input
		if(!inherits(cell.labels, "character") \|
		!inherits(labels.1, "character") \| !inherits(labels.2, "character")){
		stop("Input parameters cell.labels, labels.1 and labels.2 must be character")
		}
		if(length(setdiff(cell.labels, c(labels.1, labels.2))) > 0){
		stop("Input parameter cell.labels contain labels not from labels.1 or labels.2")
		warning("Input parameter cell.labels contain labels not from labels.1 or labels.2, subsetting...")
		cell.idx <- which(cell.labels %in% c(labels.1, labels.2))
		X <- X[cell.idx,]
		cell.labels <- cell.labels[cell.idx]
		} else {
		cell.idx <- seq_len(length(cell.labels))
		}

		if(is.null(min.cell)){
		min.cell <- as.integer(colnames(da.cells$da.ratio)[1])
		cat("Using min.cell = ", min.cell, "\n", sep = "")
		}

		n.cells <- nrow(X)
		n.dims <- ncol(X)
		if(is.null(rownames(X))){
		rownames(X) <- paste("C",c(1:n.cells), sep = "")
		}

		seurat.version <- substr(packageVersion("Seurat"),1,1)
		if(seurat.version == "3" \| seurat.version == "4"){
		X.S <- CreateSeuratObject(counts = t(X))
		@@ -146,6 +155,7 @@ getDAregion <- function(
		warning("plot.embedding must be provided by user if do.plot = T")
		X.region.plot <- NULL
		} else if(do.plot & !is.null(plot.embedding)){
		plot.embedding <- plot.embedding[cell.idx,]
		X.da.label <- da.region.label
		X.da.order <- order(X.da.label, decreasing = F)
		X.region.plot <- plotCellLabel(
		@@ -157,6 +167,7 @@ getDAregion <- function(
		}

		return(list(
		cell.idx = cell.idx,
		da.region.label = da.region.label,
		DA.stat = X.da.stat,
		da.region.plot = X.region.plot

man/getDAcells.Rd

+1 −0

Original line number	Diff line number	Diff line
		@@ -43,6 +43,7 @@ default True}
		\value{
		a list of results
		\describe{
		\item{cell.idx}{index of cells used in DA calculation}
		\item{da.ratio}{score vector for each cell}
		\item{da.pred}{(mean) prediction from the logistic regression}
		\item{da.up}{index for DA cells more abundant in condition of labels.2}

man/getDAregion.Rd

+1 −0

Original line number	Diff line number	Diff line
		@@ -41,6 +41,7 @@ getDAregion(X, da.cells, cell.labels, labels.1, labels.2,
		\value{
		a list of results
		\describe{
		\item{cell.idx}{index of cells used in DA calculation}
		\item{da.region.label}{DA region label for each cell from the whole dataset,
		'0' represents non-DA cells.}
		\item{DA.stat}{a table showing DA score and p-value for each DA region}

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