update documentation and tests to reflect filtering of links

abbvie-external · Jan 29, 2024 · 0d3f8b2 · 0d3f8b2
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Showing 4 changed files with 5 additions and 3 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,5 @@
+* limit links returned from `getEnrichmentsNetwork` to those with overlap coefficient <= .1 
+
 # 1.13.17
 
 * The release tarball includes version 1.9.0 of the web app

diff --git a/R/app.R b/R/app.R
@@ -152,7 +152,7 @@ getEnrichmentsTable <- function(study, modelID, annotationID, type = "nominal",
 #'   \item{nodes}{(data frame) The description of each annotation term (i.e.
 #'   node). The nominal and adjusted p-values are in list-columns.}
 #'   \item{links}{(list) The statistics for each pairwise overlap between the
-#'   annotation terms (i.e. nodes)}
+#'   annotation terms (i.e. nodes). This list is filtered to all links where overlap coefficient >= .1.}
 #'
 #' @importFrom data.table ":=" "%chin%" .N
 #' @export

diff --git a/inst/tinytest/testApp.R b/inst/tinytest/testApp.R
@@ -306,7 +306,7 @@ if (getRversion() >= "3.6.0") {
 
   expect_identical_xl(
     dim(enrichmentsNetwork[["links"]]),
-    as.integer(c(1020, 6))
+    as.integer(c(944, 6))
   )
 
   link1 <- structure(

diff --git a/man/getEnrichmentsNetwork.Rd b/man/getEnrichmentsNetwork.Rd