Merge pull request #91 from BodenmillerGroup/build_revert

Revert changes and add test
BodenmillerGroup · Mar 21, 2024 · a985bd6 · a985bd6
2 parents fd4b913 + a754793
commit a985bd6
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: cytomapper
-Version: 1.15.3
+Version: 1.15.4
 Title: Visualization of highly multiplexed imaging data in R
 Description: 
     Highly multiplexed imaging acquires the single-cell expression of

diff --git a/NEWS b/NEWS
@@ -195,3 +195,6 @@ Changes in version 1.15.2 (2023-12-13):
 
 Changes in version 1.15.3 (2024-03-13):
 + measureObject fixes for Bioc 3.19 release
+
+Changes in version 1.15.4 (2024-03-21):
++ measureObject fix reversion and test - Bioc 3.19
diff --git a/R/measureObjects.R b/R/measureObjects.R
@@ -254,8 +254,8 @@ measureObjects <- function(mask,
     cur_colData <- colData(object)
     cur_df <- cbind(mcols(image), mcols(mask))
     cur_df <- cur_df[,unique(names(cur_df)), drop=FALSE]
-    cur_colData <- merge(as.data.frame(as.matrix(cur_colData)), 
-                         as.data.frame(as.matrix(cur_df)), 
+    cur_colData <- merge(as.data.frame(cur_colData), 
+                         as.data.frame(cur_df), 
                          by = img_id, sort = FALSE)
     colData(object) <- as(cur_colData, "DataFrame")
 

diff --git a/tests/testthat/test_measureObjects.R b/tests/testthat/test_measureObjects.R
@@ -237,6 +237,11 @@ test_that("measureObjects: defaults work", {
                                        feature_types = c("basic", "haralick"), haralick_feature = c("var.s1", "test"), haralick_scales = c(1, 3)),
                  regexp = "Only haralick features of type asm.s1, con.s1, cor.s1, var.s1, idm.s1, sav.s1, sva.s1, sen.s1, ent.s1, dva.s1, den.s1, f12.s1, f13.s1, asm.s3, con.s3, cor.s3, var.s3, idm.s3, sav.s3, sva.s3, sen.s3, ent.s3, dva.s3, den.s3, f12.s3, f13.s3 allowed.",
                  fixed = TRUE)
+
+    # Test for character img_id
+    expect_silent(sce <- measureObjects(pancreasMasks, pancreasImages, img_id = "ImageName"))
+    expect_true(is.numeric(sce$object_id))
+    expect_equal(sce$object_id[1:10], c(824, 835, 839, 844, 847, 853, 859, 864, 865, 872))
 })
 
 test_that("measureObjects: different settings work", {