diff --git a/R/visualization.R b/R/visualization.R index 7a73a79..077ae71 100644 --- a/R/visualization.R +++ b/R/visualization.R @@ -3237,7 +3237,7 @@ netVisual_embeddingPairwise <- function(object, slot.name = "netP", type = c("fu if (is.null(pathway.remove)) { similarity <- methods::slot(object, slot.name)$similarity[[type]]$matrix[[comparison.name]] pathway.remove <- rownames(similarity)[which(colSums(similarity) == 1)] - pathway.remove <- sub("--.*", "", pathway.remove) + # pathway.remove <- sub("--.*", "", pathway.remove) } if (length(pathway.remove) > 0) { @@ -3353,13 +3353,14 @@ netVisual_embeddingPairwiseZoomIn <- function(object, slot.name = "netP", type = if (is.null(pathway.remove)) { similarity <- methods::slot(object, slot.name)$similarity[[type]]$matrix[[comparison.name]] pathway.remove <- rownames(similarity)[which(colSums(similarity) == 1)] - pathway.remove <- sub("--.*", "", pathway.remove) + # pathway.remove <- sub("--.*", "", pathway.remove) } if (length(pathway.remove) > 0) { for (i in 1:length(prob)) { probi <- prob[[i]] - pathway.remove.idx <- which(dimnames(probi)[[3]] %in% pathway.remove) + pathway.remove.idx <- which(paste0(dimnames(probi)[[3]],"--",object.names[i]) %in% pathway.remove) + # pathway.remove.idx <- which(dimnames(probi)[[3]] %in% pathway.remove) if (length(pathway.remove.idx) > 0) { probi <- probi[ , , -pathway.remove.idx] }