update GPU setting (d0c494f1) · Commits · github_fork / DAseq2

R/STGmarkerFinder.R

+3 −3

Original line number	Diff line number	Diff line
		@@ -43,11 +43,11 @@ STGmarkerFinder <- function(
		# set Python
		use_python(python = python.use, required = T)

		source_python(file = paste(system.file(package="DAseq"), "DA_STG.py", sep = "/"))

		# set GPU device
		py_run_string(paste("os.environ['CUDA_VISIBLE_DEVICES'] = '", GPU, "'", sep = ""))

		source_python(file = paste(system.file(package="DAseq"), "DA_STG.py", sep = "/"))

		# turn X into Python format
		X.py <- r_to_py(as.matrix(X))

		@@ -164,8 +164,8 @@ runSTG <- function(
		){
		# set Python
		use_python(python = python.use, required = T)
		py_run_string(paste("os.environ['CUDA_VISIBLE_DEVICES'] = '", GPU, "'", sep = ""))
		source_python(file = paste(system.file(package="DAseq"), "DA_STG.py", sep = "/"))
		py_run_string(paste("os.environ['CUDA_VISIBLE_DEVICES'] = '", GPU, "'", sep = ""))

		if(!is.null(label.2)){
		X.use <- which(X.labels %in% c(label.1,label.2))

+4 −4

Original line number	Diff line number	Diff line
		@@ -42,6 +42,7 @@ getDAcells <- function(
		do.plot = T, plot.embedding = NULL, size = 0.5,
		python.use = "/usr/bin/python", GPU = ""
		){
		# cat("Using GPU ", GPU, ".\n", sep = "")

		# get DA score vector for each cell
		cat("Calculating DA score vector.\n")
		@@ -64,16 +65,15 @@ getDAcells <- function(
		binary.labels_py <- r_to_py(as.matrix(binary.labels))
		X.knn.ratio_py <- r_to_py(as.matrix(X.knn.ratio))


		# set GPU device
		py_run_string(paste("os.environ['CUDA_VISIBLE_DEVICES'] = '", GPU, "'", sep = ""))

		# get neural network predictions for each cell
		cat("Running logistic regression.\n")
		source_python(file = paste(system.file(package="DAseq"), "DA_logit.py", sep = "/"))
		# py_run_string(paste("epochs = ", epochs, sep = ""))
		py_run_string(paste("k_folds = ", k.folds, sep = ""))

		# set GPU device
		py_run_string(paste("os.environ['CUDA_VISIBLE_DEVICES'] = '", GPU, "'", sep = ""))


		# check n.runs
		if(n.runs == 1){