Merge pull request #91 from BodenmillerGroup/build_revert

Revert changes and add test

Author: lassedochreden

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

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

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")
 

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", {