Merge branch 'release-1.2.2'

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: DIscBIO
-Date: 2023-10-09
+Date: 2023-11-06
 Title: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
-Version: 1.2.1
+Version: 1.2.2
 Authors@R:
   c(
     person(
@@ -39,7 +39,7 @@ Description: An open, multi-algorithmic pipeline for easy, fast and efficient
 License: MIT + file LICENSE
 Encoding: UTF-8
 Imports: methods, TSCAN, httr, mclust, statmod, igraph,
-  RWeka, philentropy, NetIndices, png, grDevices,
+  RWeka, vegan, NetIndices, png, grDevices,
   RColorBrewer, ggplot2, rpart, fpc, cluster, rpart.plot,
   tsne, AnnotationDbi, org.Hs.eg.db, graphics, stats, utils, impute,
   withr

NAMESPACE

@@ -110,7 +110,6 @@ importFrom(mclust,mclustBIC)
 importFrom(methods,is)
 importFrom(methods,new)
 importFrom(methods,validObject)
-importFrom(philentropy,distance)
 importFrom(png,readPNG)
 importFrom(rpart,rpart)
 importFrom(rpart.plot,rpart.plot)
@@ -142,6 +141,7 @@ importFrom(utils,download.file)
 importFrom(utils,read.table)
 importFrom(utils,write.csv)
 importFrom(utils,write.table)
+importFrom(vegan,vegdist)
 importFrom(withr,local_options)
 importFrom(withr,with_options)
 importFrom(withr,with_par)

NEWS.md

@@ -1,3 +1,7 @@
+# DIscBIO 1.2.2
+
+* Fixed calculation of Jaccard index (issue #44)
+
 # DIscBIO 1.2.1
 
 * Fixed integration and unit tests (issue #22, #37)

R/Jaccard.R

@@ -10,7 +10,6 @@
 #' @param K A numeric value of the number of clusters
 #' @param plot if `TRUE`, plots the mean Jaccard similarities
 #' @param R number of bootstrap replicates
-#' @importFrom philentropy distance
 #' @importFrom graphics barplot box
 #' @return A plot of the mean Jaccard similarity coefficient per cluster.
 Jaccard <- function(object, Clustering = "K-means", K, plot = TRUE, R = 100) {

R/bootstrap.R

@@ -11,10 +11,10 @@ bootstrap <- function(data, n_reps) {
   return(results)
 }
 
+#' @importFrom vegan vegdist
 JS <- function(data, indices) {
   d <- data[indices, ]
-  jac <- suppressMessages(distance(t(d), method = "jaccard"))
+  jac <- vegan::vegdist(d, method = "jaccard")
   jac1 <- 1 - jac
-  JSmean <- mean(jac1)
-  return(JSmean)
+  return(mean(jac1))
 }

tests/testthat/test-MRE.R

@@ -66,7 +66,7 @@ test_that("tSNE is computed", {
 test_that("Cluster plots output is as expexted", {
   expect_equivalent(
     object = Jaccard(sc, Clustering = "K-means", K = 2, plot = FALSE, R = 5),
-    expected = c(.417, .413),
+    expected = c(.683, .624),
     tolerance = .01
   )
   expect_equal(