fix documentation of reduceSimMatrix

imbforge · Oct 17, 2023 · a75afc9 · a75afc9
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rrvgo
 Type: Package
 Title: Reduce + Visualize GO
-Version: 1.13.1
+Version: 1.13.2
 Authors@R: c(person("Sergi", "Sayols", email = "[email protected]", role = c("aut", "cre")), person("Sara", "Elmeligy", role = "ctb"))
 Description: Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.
 URL: https://www.bioconductor.org/packages/rrvgo, https://ssayols.github.io/rrvgo/index.html

diff --git a/R/rrvgo.R b/R/rrvgo.R
@@ -66,15 +66,17 @@ calculateSimMatrix <- function(x,
 #' Reduce a set of GO terms based on their semantic similarity and scores.
 #' 
 #' @details
+#' Remove terms with a similarity below `threshold`. Decide which term
+#' remains based on a score. If no score is provided, then decide based on the
+#' "uniqueness" or the term "size".
+#'
 #' Currently, rrvgo uses the similarity between pairs of terms to compute a 
 #' distance matrix, defined as (1-simMatrix). The terms are then hierarchically 
 #' clustered using complete linkage, and the tree is cut at the desired threshold, 
 #' picking the term with the highest score as the representative of each group.  
 #' 
 #' Therefore, higher thresholds lead to fewer groups, and the threshold should be 
-#' read as the expected similarity of terms within a group (though this is not 
-#' entirely correct, and you'll see similarities below this threshold being put in 
-#' the same group).
+#' read as the minimum similarity between group representatives.
 #' 
 #' @param simMatrix a (square) similarity matrix
 #' @param scores one of c("uniqueness", "size"), or a *named* vector with scores

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/rrvgo.html b/docs/articles/rrvgo.html
diff --git a/docs/articles/rrvgo_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/rrvgo_files/figure-html/unnamed-chunk-4-1.png
diff --git a/docs/articles/rrvgo_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/rrvgo_files/figure-html/unnamed-chunk-6-1.png
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   rrvgo: rrvgo.html
-last_built: 2023-09-06T20:29Z
+last_built: 2023-10-17T11:11Z
 
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
diff --git a/docs/reference/calculateSimMatrix.html b/docs/reference/calculateSimMatrix.html
diff --git a/docs/reference/getGoSize.html b/docs/reference/getGoSize.html
diff --git a/docs/reference/getGoTerm.html b/docs/reference/getGoTerm.html
diff --git a/docs/reference/getTermDisp.html b/docs/reference/getTermDisp.html
diff --git a/docs/reference/getTermUniq.html b/docs/reference/getTermUniq.html
diff --git a/docs/reference/gg_color_hue.html b/docs/reference/gg_color_hue.html
diff --git a/docs/reference/heatmapPlot.html b/docs/reference/heatmapPlot.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/loadOrgdb.html b/docs/reference/loadOrgdb.html
diff --git a/docs/reference/reduceSimMatrix.html b/docs/reference/reduceSimMatrix.html
diff --git a/docs/reference/scatterPlot-1.png b/docs/reference/scatterPlot-1.png