diff --git a/R/clustering.R b/R/clustering.R index a87088b..61c8708 100644 --- a/R/clustering.R +++ b/R/clustering.R @@ -946,7 +946,7 @@ degMDS = function(counts, condition=NULL, k=2, d="euclidian", xi=1, yi=2) { #' @param plot boolean plot the clusters found #' @param fixy vector integers used as ylim in plot #' @param nClusters an integer scalar or vector with the desired number of groups -#' @param skipDendo a boolean to run or not dendextend. Temporary fix to memory +#' @param skipDendrogram a boolean to run or not dendextend. Temporary fix to memory #' issue in linux. #' @details #' It can work with one or more groups with 2 or @@ -1138,7 +1138,7 @@ degPatterns = function(ma, metadata, minc=15, summarize="merge", } dend_plot <- NA - if (length(unique(groups)) > 0 & is.null(nClusters) & !skipDendo){ + if (length(unique(groups)) > 0 & is.null(nClusters) & !skipDendrogram){ dend <- cluster_genes h = dend$dc clust <- cutree(as.hclust(dend), h = h) @@ -1155,7 +1155,7 @@ degPatterns = function(ma, metadata, minc=15, summarize="merge", if (plot) plot(dend_plot, xlab="", ylab="", main="", sub="", axes=FALSE, cex = 2) } - if (length(unique(groups)) > 0 & is.numeric(nClusters) & !skipDendo){ + if (length(unique(groups)) > 0 & is.numeric(nClusters) & !skipDendrogram){ dend <- cluster_genes clust <- cutree(as.hclust(dend), k = nClusters) clust.cutree <- dendextend::cutree(dend, k = nClusters, order_clusters_as_data = FALSE) diff --git a/man/degPatterns.Rd b/man/degPatterns.Rd index 94d0792..66c34dd 100644 --- a/man/degPatterns.Rd +++ b/man/degPatterns.Rd @@ -20,7 +20,8 @@ degPatterns( eachStep = FALSE, plot = TRUE, fixy = NULL, - nClusters = NULL + nClusters = NULL, + skipDendo = TRUE ) } \arguments{ @@ -75,6 +76,9 @@ with multiple time points}.} \item{fixy}{vector integers used as ylim in plot} \item{nClusters}{an integer scalar or vector with the desired number of groups} + +\item{skipDendrogram}{a boolean to run or not dendextend. Temporary fix to memory +issue in linux.} } \value{ list wiht two items: