add mean.adj as an option for blend

R/RunCellToSystem.R

@@ -12,7 +12,7 @@
 #' @param sys.small A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.
 #' @param ground.truth Ground truth signaling mechanisms present in sys.small.
 #' @param assay The assay to run the CellToSystem transformation on. Defaults to "RNA."
-#' @param blend Choice of linear operator to combine edges. Defaults to "mean", also accepts "sum"
+#' @param blend Choice of linear operator to combine edges. Defaults to "mean", also accepts "sum","mean.adj"
 #' @param meta.data.to.map A character vector of metadata names present in the original object which will be carried to the NICHES objects
 #' @param output_format string. Choice of the output format. "seurat" will output a list of seurat objects, "raw" will output a list of lists with raw interaction matrix and compiled metadata
 #' 
@@ -50,6 +50,12 @@ RunCellToSystem <- function(sys.small,
   if (blend == 'mean'){
     rec.map2 <- Matrix::rowMeans(rec.map,dims = 1)
   }
+  if (blend == 'mean.adj'){
+    binary <- rec.map > 0
+    percent.expression <- Matrix::rowSums(binary)/ncol(binary)
+    rec.map2 <- Matrix::rowMeans(rec.map,dims=1)
+    rec.map2 <- rec.map2/percent.expression
+  }
   rec.map2 <- do.call(cbind, replicate(ncol(rec.map), rec.map2, simplify=FALSE))
 
   # Ligand data

R/RunSystemToCell.R

@@ -12,7 +12,7 @@
 #' @param sys.small A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings. 
 #' @param ground.truth Ground truth signaling mechanisms present in sys.small.
 #' @param assay The assay to run the SystemToCell transformation on. Defaults to "RNA."
-#' @param blend Choice of linear operator to combine edges. Defaults to "mean", also accepts "sum"
+#' @param blend Choice of linear operator to combine edges. Defaults to "mean", also accepts "sum", "mean.adj"
 #' @param meta.data.to.map A character vector of metadata names present in the original object which will be carried to the NICHES objects
 #' @param output_format string. Choice of the output format. "seurat" will output a list of seurat objects, "raw" will output a list of lists with raw interaction matrix and compiled metadata
 #'
@@ -49,6 +49,12 @@ RunSystemToCell <- function(sys.small,
   if (blend == 'mean'){
     lig.map2 <- Matrix::rowMeans(lig.map,dims = 1)
   }
+  if (blend == 'mean.adj'){
+    binary <- lig.map > 0
+    percent.expression <- Matrix::rowSums(binary)/ncol(binary)
+    lig.map2 <- Matrix::rowMeans(lig.map,dims=1)
+    lig.map2 <- lig.map2/percent.expression
+  }
   lig.map2 <- do.call(cbind, replicate(ncol(lig.map), lig.map2, simplify=FALSE))
 
   # Receptor data