some improvements

R/RNAMagnet.R

@@ -85,7 +85,7 @@ RNAMagnetBase <- function(seurat, anchors=NULL,neighborhood.distance=NULL, neigh
   out <- new("rnamagnet", celltype = seurat@ident, params = list("neighborhood.distance"=neighborhood.distance, "neighborhood.gradient" =neighborhood.gradient, ".k" = .k, ".x0" = .x0, ".minExpression" = .minExpression, ".cellularCompartment" = .cellularCompartment, ".manualAnnotation" = .manualAnnotation, ".symmetric" = .symmetric))
 
   #compute cell-cell similarity
-  out@similarity <- as.matrix(1-cor(t(seurat@dr$pca@cell.embeddings[,1:15])))
+  similarity <- as.matrix(1-cor(t(seurat@dr$pca@cell.embeddings[,1:15])))
 
   #prepare database
   ligrec <- getLigandsReceptors(.version, .cellularCompartment, .manualAnnotation)
@@ -148,7 +148,7 @@ RNAMagnetBase <- function(seurat, anchors=NULL,neighborhood.distance=NULL, neigh
   out@specificity <- t(sapply(rownames(out@interaction), function(cell) {
     x <- out@interaction[cell,]
     beta <- x/sum(x)
-    if (!is.null(neighborhood.distance)) alpha <- apply(out@interaction * (1-kernel(out@similarity[cell,],neighborhood.gradient,x0=neighborhood.distance )),2,sum) else alpha <- apply(out@interaction,2,mean)
+    if (!is.null(neighborhood.distance)) alpha <- apply(out@interaction * (1-kernel(similarity[cell,],neighborhood.gradient,x0=neighborhood.distance )),2,sum) else alpha <- apply(out@interaction,2,mean)
     alpha <- alpha / sum(alpha)
     beta- alpha
   }))

R/plotfunctions.R

@@ -5,9 +5,16 @@
 #'@param threshold Threshold interaction strength for including an edge in the network.
 #'@param colors A named vector of colors to be used for plotting; names correspond to levels of \code{rnamagnet@class}
 #'@param useLabels Plot the population labels on the graph?
+#'@param ... Parameters passed to \code{\link[igraph]{plot.igraph}}, e.g. a layout can be stored as described in the example code below
+#'@examples
+#'\dontrun{
+#'network <- PlotSignalingNetwork(rnamagnet_result)
+#'layout <- layout_nicely(network)
+#'PlotSignalingNetwork(rnamagnet_result, layout = layout)
+#'}
 #'@return Plots the network and invisibly returns an object of class \code{\link[igraph]{igraph}}
 #'@export
-PlotSignalingNetwork <- function(rnamagnet, threshold = 0.01, colors = NULL, useLabels=T) {
+PlotSignalingNetwork <- function(rnamagnet, threshold = 0.01, colors = NULL, useLabels=T, ...) {
 
   pops <- colnames(rnamagnet@specificity)
   mean_by_pop <- sapply(pops, function(id) {
@@ -30,7 +37,7 @@ if(!is.null(colors)){
   graphf$color <- colors[graphf$sender]
 }
 
-  plotgraph <- igraph::graph_from_data_frame(subset(graphf,value > 0.01 ), vertices = vertices)
-  if (useLabels) plot(plotgraph,vertex.frame.color=NA, edge.arrow.mode = "-",  edge.curved=0.3) else plot(plotgraph,vertex.frame.color=NA, edge.arrow.mode = "-", vertex.label = NA, edge.curved=0.3)
+  plotgraph <- igraph::graph_from_data_frame(subset(graphf,value > threshold ), vertices = vertices)
+  if (useLabels) plot(plotgraph,vertex.frame.color=NA, edge.arrow.mode = "-",  edge.curved=0.3, ...) else plot(plotgraph,vertex.frame.color=NA, edge.arrow.mode = "-", vertex.label = NA, edge.curved=0.3, ...)
   invisible(plotgraph)
 }

R/rnamagnet-class.R

@@ -3,7 +3,6 @@
 #'
 #'This class contains representation for the output of \code{\link{RNAMagnetBase}}.
 #'
-#'@slot similarity Cell-cell distance matrix
 #'@slot anchors Mean gene expression matrix of anchor populations
 #'@slot interaction Interaction score matrix between cells and anchor populations
 #'@slot specificity Specificity of interaction scores relative to similar cells
@@ -16,7 +15,6 @@ rnamagnet <- setClass(
   "rnamagnet",
   slots = c(
     anchors = "matrix",
-    similarity = "matrix",
     weight = "matrix",
     interaction = "matrix",
     specificity = "matrix",