Commit fe55fa26 authored by Lars Velten's avatar Lars Velten
Browse files

closed a bracked

parent 6c11ec7e
......@@ -32,7 +32,7 @@
#' geom_point(color = "black", shape = 17, size= 3, data=plf[use,])
#'}
#'@export
RNAMagnetAnchors <- function(seurat, anchors, return = "summary", neighborhood.distance = 0.7, neighborhood.gradient = 3, .k = 10, .x0 = 0.5, .minExpression = 0, .version = "latest", .cellularCompartment = c("Membrane","ECM","Both"), .manualAnnotation = "Correct" ) {
RNAMagnetAnchors <- function(seurat, anchors, return = "summary", neighborhood.distance = 0.7, neighborhood.gradient = 3, .k = 10, .x0 = 0.5, .minExpression = 0, .version = "1.0.0", .cellularCompartment = c("Membrane","ECM","Both"), .manualAnnotation = "Correct" ) {
myMagnet <- RNAMagnetBase(seurat, anchors, neighborhood.distance,neighborhood.gradient, .k, .x0, .minExpression, .version, .cellularCompartment, .manualAnnotation,TRUE)
if (return=="rnamagnet-class") myMagnet else data.frame(direction = as.factor(colnames(myMagnet@specificity)[apply(myMagnet@specificity,1,which.max)]), adhesiveness = myMagnet@adhesiveness, myMagnet@specificity[,anchors])
......@@ -46,7 +46,7 @@ RNAMagnetAnchors <- function(seurat, anchors, return = "summary", neighborhood.d
#'@param ... For explanation of all further parameters, see \code{\link{RNAMagnetBase}}.
#'@return Returns an objects of class \code{\link{rnamagnet}}. \code{\link{PlotSignalingNetwork}} or \code{\link{getRNAMagnetGenes}} can be used for further analyses.
#'@export
RNAMagnetSignaling <- function(seurat, neighborhood.distance = NULL, neighborhood.gradient = NULL, .k = 10, .x0 = 0.5, .minExpression = 10, .version = "latest", .cellularCompartment = c("Secreted","Both"), .manualAnnotation = "Correct" ) {
RNAMagnetSignaling <- function(seurat, neighborhood.distance = NULL, neighborhood.gradient = NULL, .k = 10, .x0 = 0.5, .minExpression = 10, .version = "1.0.0", .cellularCompartment = c("Secreted","Both"), .manualAnnotation = "Correct" ) {
RNAMagnetBase(seurat, anchors = NULL, neighborhood.distance,neighborhood.gradient, .k, .x0, .minExpression, .version, .cellularCompartment, .manualAnnotation, FALSE)
......@@ -81,7 +81,7 @@ RNAMagnetSignaling <- function(seurat, neighborhood.distance = NULL, neighborhoo
#'@details Add the methods section of the paper here!
#'@return Returns an object of class \code{\link{rnamagnet}}
#'@export
RNAMagnetBase <- function(seurat, anchors=NULL,neighborhood.distance=NULL, neighborhood.gradient =NULL, .k = 10, .x0 = 0.5, .minExpression, .version = "latest", .cellularCompartment, .manualAnnotation = "Correct", .symmetric = F) {
RNAMagnetBase <- function(seurat, anchors=NULL,neighborhood.distance=NULL, neighborhood.gradient =NULL, .k = 10, .x0 = 0.5, .minExpression, .version = "1.0.0", .cellularCompartment, .manualAnnotation = "Correct", .symmetric = F) {
cat("Setting everything up...\n")
if (grepl("^3", Biobase::package.version("Seurat"))) {
......
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