From 0a6579e40dd5c7becaf9e6a880e35dbb9b190db9 Mon Sep 17 00:00:00 2001 From: Stefano Mangiola Date: Thu, 20 May 2021 12:31:25 +1000 Subject: [PATCH 1/4] Update modeling.R --- R/modeling.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/modeling.R b/R/modeling.R index 2db536d..fafca85 100644 --- a/R/modeling.R +++ b/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] From 1902dec6fd396efde30673644d7d5f5979ff25c7 Mon Sep 17 00:00:00 2001 From: Stefano Mangiola Date: Thu, 20 May 2021 15:07:22 +1000 Subject: [PATCH 2/4] Update analysis.R --- R/analysis.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/analysis.R b/R/analysis.R index ee02b79..fe3efa1 100644 --- a/R/analysis.R +++ b/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!") From 90611d74ebc7ae6c429acae18f7b7bacfa40f2ac Mon Sep 17 00:00:00 2001 From: Stefano Mangiola Date: Thu, 20 May 2021 15:15:03 +1000 Subject: [PATCH 3/4] Update analysis.R --- R/analysis.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/analysis.R b/R/analysis.R index fe3efa1..77583bb 100644 --- a/R/analysis.R +++ b/R/analysis.R @@ -981,7 +981,7 @@ rankNet <- function(object, slot.name = "netP", mode = c("comparison", "single") } } idx.t <- setdiff(1:nrow(prob), sources.use) - prob[idx.t, , ] <- 0 + prob[idx.t, , ,drop=FALSE] <- 0 } if (!is.null(targets.use)) { if (is.character(targets.use)) { From f7761e58d7d9dd0bc712d342b842115062c7b122 Mon Sep 17 00:00:00 2001 From: Stefano Mangiola Date: Thu, 20 May 2021 15:32:07 +1000 Subject: [PATCH 4/4] Update modeling.R --- R/modeling.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/modeling.R b/R/modeling.R index fafca85..fad8c70 100644 --- a/R/modeling.R +++ b/R/modeling.R @@ -378,7 +378,7 @@ computeCommunProbPathway <- function(object = NULL, net = NULL, pairLR.use = NUL 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] + prob.pathways.sig <- prob.pathways.sig[, , idx, drop=FALSE] if (is.null(object)) { netP = list(pathways = pathways.sig, prob = prob.pathways.sig)