Update modeling.R

R/analysis.R

@@ -49,7 +49,7 @@ netAnalysis_contribution <- function(object, signaling, signaling.name = NULL, w
     pairLR <- pairLR[pairLR.name.use,]
   }
 
-  prob <- prob[,,pairLR.name.use]
+  prob <- prob[,,pairLR.name.use, drop=FALSE]
 
   if (length(dim(prob)) == 2) {
     prob <- replicate(1, prob, simplify="array")
@@ -992,7 +992,7 @@ rankNet <- function(object, slot.name = "netP", mode = c("comparison", "single")
         }
       }
       idx.t <- setdiff(1:nrow(prob), targets.use)
-      prob[ ,idx.t, ] <- 0
+      prob[ ,idx.t, ,drop=FALSE] <- 0
     }
     if (sum(prob) == 0) {
       stop("No inferred communications for the input!")
@@ -1058,7 +1058,7 @@ rankNet <- function(object, slot.name = "netP", mode = c("comparison", "single")
           }
         }
         idx.t <- setdiff(1:nrow(prob), targets.use)
-        prob[ ,idx.t, ] <- 0
+        prob[ ,idx.t, , drop=FALSE] <- 0
       }
       if (sum(prob) == 0) {
         stop("No inferred communications for the input!")

R/modeling.R

@@ -375,7 +375,7 @@ computeCommunProbPathway <- function(object = NULL, net = NULL, pairLR.use = NUL
   group <- factor(pairLR.use$pathway_name, levels = pathways)
   prob.pathways <- aperm(apply(prob, c(1, 2), by, group, sum), c(2, 3, 1))
   pathways.sig <- pathways[apply(prob.pathways, 3, sum) != 0]
-  prob.pathways.sig <- prob.pathways[,,pathways.sig]
+  prob.pathways.sig <- prob.pathways[,,pathways.sig, drop=FALSE]
   idx <- sort(apply(prob.pathways.sig, 3, sum), decreasing=TRUE, index.return = TRUE)$ix
   pathways.sig <- pathways.sig[idx]
   prob.pathways.sig <- prob.pathways.sig[, , idx]