update STG (189b0790) · Commits · github_fork / DAseq2

R/STGmarkerFinder.R

+13 −4

Original line number	Diff line number	Diff line
		@@ -69,7 +69,7 @@ STGmarkerFinder <- function(
		da.model <- list()
		for(ii in da.regions.to.run){
		# prepare labels
		da.label.bin <- (da.label == ii)
		da.label.bin <- as.numeric(da.label == ii)
		da.label.bin.py <- r_to_py(as.matrix(da.label.bin))
		da.label.bin.py <- da.label.bin.py$flatten()

		@@ -127,11 +127,13 @@ STGmarkerFinder <- function(

		#' Run STG
		#'
		#' Run STG to select a set of genes that separate cells with one label from the other label
		#' Run STG to select a set of genes that separate cells with label.1 from label.2 (other labels)
		#'
		#' @param X matrix, normalized expression matrix of all cells in the dataset, genes are in rows,
		#' rownames must be gene names
		#' @param X.labels numeric vector, specify labels for each cell, must be 0 or 1
		#' @param label.1 cell label to define markers for
		#' @param label.2 second cell label to for comparison, if NULL, use all other labels
		#' @param lambda numeric, regularization parameter that weights the number of selected genes,
		#' a larger lambda leads to fewer genes, default 1.5
		#' @param n.runs integer, number of runs to run the model, default 5
		@@ -156,16 +158,23 @@ STGmarkerFinder <- function(
		#' @export
		#'
		runSTG <- function(
		X, X.labels, lambda = 1.5, n.runs = 5, return.model = F,
		X, X.labels, label.1, label.2 = NULL,
		lambda = 1.5, n.runs = 5, return.model = F,
		python.use = "/usr/bin/python", GPU = ""
		){
		# set Python
		use_python(python = python.use, required = T)
		source_python(file = paste(system.file(package="DAseq"), "DA_STG.py", sep = "/"))

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

		X.py <- r_to_py(as.matrix(X))

		X.label.bin <- (X.labels == 1)
		X.label.bin <- as.numeric(X.labels == label.1)
		X.label.bin.py <- r_to_py(as.matrix(X.label.bin))
		X.label.bin.py <- X.label.bin.py$flatten()

man/runSTG.Rd

+8 −3

Original line number	Diff line number	Diff line
		@@ -4,8 +4,9 @@
		\alias{runSTG}
		\title{Run STG}
		\usage{
		runSTG(X, X.labels, lambda = 1.5, n.runs = 5, return.model = F,
		python.use = "/usr/bin/python", GPU = "")
		runSTG(X, X.labels, label.1, label.2 = NULL, lambda = 1.5,
		n.runs = 5, return.model = F, python.use = "/usr/bin/python",
		GPU = "")
		}
		\arguments{
		\item{X}{matrix, normalized expression matrix of all cells in the dataset, genes are in rows,
		@@ -13,6 +14,10 @@ rownames must be gene names}

		\item{X.labels}{numeric vector, specify labels for each cell, must be 0 or 1}

		\item{label.1}{cell label to define markers for}

		\item{label.2}{second cell label to for comparison, if NULL, use all other labels}

		\item{lambda}{numeric, regularization parameter that weights the number of selected genes,
		a larger lambda leads to fewer genes, default 1.5}

		@@ -38,5 +43,5 @@ a list of results:
		}
		}
		\description{
		Run STG to select a set of genes that separate cells with one label from the other label
		Run STG to select a set of genes that separate cells with label.1 from label.2 (other labels)
		}

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