From d9725783371d72c54e4db8d46c9dcfcbe74afb01 Mon Sep 17 00:00:00 2001 From: lassedochreden Date: Thu, 21 Mar 2024 11:40:23 +0000 Subject: [PATCH 1/2] revert as.matrix and add test --- R/measureObjects.R | 4 ++-- tests/testthat/test_measureObjects.R | 5 +++++ 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/R/measureObjects.R b/R/measureObjects.R index d0b57a5..55513c7 100644 --- 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 index 5e7775c..6ecf7c0 100644 --- 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", { From a7547932e9a50ea8ffea553b2aa0d9795869a3ca Mon Sep 17 00:00:00 2001 From: lassedochreden Date: Thu, 21 Mar 2024 11:42:39 +0000 Subject: [PATCH 2/2] news and descp bump --- DESCRIPTION | 2 +- NEWS | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d551e30..8085116 100644 --- 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 index c31bda4..a1fa264 100644 --- 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