roxygenize umap scatterPlot

Author: ssayols

DESCRIPTION

@@ -54,6 +54,6 @@ Suggests:
     org.Ss.eg.db,
     org.Xl.eg.db
 VignetteBuilder: knitr
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.0
 biocViews: Annotation, Clustering, GO, Network, Pathways, Software
 NeedsCompilation: no

NAMESPACE

@@ -26,4 +26,5 @@ importFrom(stats,setNames)
 importFrom(tm,Corpus)
 importFrom(tm,TermDocumentMatrix)
 importFrom(treemap,treemap)
+importFrom(umap,umap)
 importFrom(wordcloud,wordcloud)

R/plotlib.R

@@ -3,10 +3,11 @@
 #' 
 #' @param simMatrix a (square) similarity matrix.
 #' @param reducedTerms a data.frame with the reduced terms from reduceSimMatrix()
+#' @param algorithm algorithm for dimensionality reduction. Either pca or umap.
 #' @param size what to use as point size. Can be either GO term's "size" or "score"
 #' @param addLabel add labels with the most representative term of the group.
 #' @param labelSize text size in the label.
-#' @return  ggplot2 object raedy to be printed (or manipulated)
+#' @return  ggplot2 object ready to be printed (or manipulated)
 #' @details  Distances between points represent the similarity between terms.
 #' Axes are the first 2 components of applying a PCoA to the (di)similarity matrix.
 #' Size of the point represents the provided scores or, in its absence, the number