Fixed code to throw errors when spatial coordinates are missing.

SydneyBioX · Nov 28, 2024 · d89f414 · d89f414
1 parent e8ac624
commit d89f414
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Showing 4 changed files with 5 additions and 30 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clustSIGNAL
 Type: Package
 Title: clustSIGNAL: a spatial clustering method
-Version: 0.99.4
+Version: 0.99.5
 Authors@R: c(
     person("Pratibha", "Panwar", email = "[email protected]", 
     role = c("cre", "aut", "ctb"), comment = c(ORCID = "0000-0002-7437-7084")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+## clustSIGNAL v0.99.5 (2024-11-28)
+* Fixed issue where absence of spatial coordinates was not throwing error at the beginning of the run.
+
 ## clustSIGNAL v0.99.4 (2024-11-28)
 * Corrected character check for output format type.
 

diff --git a/R/clustSIGNAL.R b/R/clustSIGNAL.R
@@ -75,7 +75,7 @@ clustSIGNAL <- function (spe, samples, cells, dimRed = "None", batch = FALSE,
                                             cluster.fun = "louvain")) {
     time_start <- Sys.time()
     # data and parameter checks
-    if (is.null(spatialCoords(spe)) == TRUE){
+    if (length(spatialCoords(spe)) == 0){
         stop("Spatial coordinates not found.")
     } else if (is.null(logcounts(spe)) == TRUE) {
         stop("Normalised gene expression not found.")

diff --git a/tests/testthat/test_conditions.R b/tests/testthat/test_conditions.R
@@ -1,31 +1,3 @@
-# test_that("Checking dimensions of neighbours matrix", {
-#     data(example)
-#     cells <- "uniqueID"
-#     samples <- "sample_id"
-#     NN <- 30
-#     out <- clustSIGNAL::neighbourDetect(spe, samples, NN, cells,
-#                                         sort = TRUE)
-#
-#     testthat::expect_equal(
-#         dim(out$nnCells),
-#         as.integer(c(ncol(spe), NN + 1))
-#     )
-# })
-#
-# test_that("Checking neighbours detected for all cells", {
-#     data(example)
-#     cells <- "uniqueID"
-#     samples <- "sample_id"
-#     NN <- 30
-#     out <- clustSIGNAL::neighbourDetect(spe, samples, NN, cells,
-#                                         sort = TRUE)
-#
-#     testthat::expect_identical(
-#         as.character(out$nnCells[, 1]),
-#         spe[[cells]]
-#     )
-# })
-
 test_that(
     "Expecting error when wrong column name given for samples", {
         data(example)