Merge branch 'devel' of github.com:LieberInstitute/visiumStitched int…

…o devel

R/prep_fiji_coords.R

@@ -7,12 +7,10 @@
 #' file from Spaceranger, and transform using the rotation matrix specified
 #' by Fiji. Write one new \code{tissue_positions.csv} file per group.
 #'
-#' @param sample_info A \code{tibble} with columns \code{capture_area},
-#' \code{group}, \code{fiji_xml_path}, \code{intra_group_scalar}, and
-#' \code{group_hires_scalef}
 #' @param out_dir A character(1) vector giving a path to a directory to place
 #' the output pixel coordinates CSVs. Provided the parent exists, \code{out_dir}
 #' will be created if necessary.
+#' @inheritParams add_array_coords
 #'
 #' @return This function returns `character()` with the file paths to the
 #' `tissue_positions.csv` files it created.

R/prep_fiji_image.R

@@ -7,15 +7,13 @@
 #' Spaceranger's. In conjunction with \code{prep_fiji_image()}, this function
 #' prepares for building the \code{SpatialExperiment} with \code{build_spe()}.
 #'
-#' @param sample_info A \code{tibble} with columns \code{capture_area},
-#' \code{group}, \code{fiji_image_path}, \code{spaceranger_dir},
-#' \code{intra_group_scalar}, and \code{group_hires_scalef}
 #' @param out_dir A character(1) vector giving a path to a directory to place
 #' the output image(s) and scale factors. Provided the parent exists, \code{out_dir}
 #' will be created if necessary.
 #' @param lowres_max_size An integer(1) vector: the resolution (number of
 #' pixels) of the larger dimension of the output image(s), considered to be "low
 #' resolution".
+#' @inheritParams add_array_coords
 #'
 #' @return This function returns `character()` with the file paths to the
 #' `tissue_lowres_image.png` and `scalefactors_json.json` files it created.

R/rescale_fiji_inputs.R

@@ -17,11 +17,10 @@
 #' (as from Spaceranger's \code{scalefactors_json.json} file) appropriate for
 #' every capture area from the group.
 #'
-#' @param sample_info A \code{tibble} with columns \code{capture_area},
-#' \code{group}, and \code{spaceranger_dir}
 #' @param out_dir A character(1) vector giving a path to a directory to place
 #' the output images. Provided the parent exists, \code{out_dir}
 #' will be created if necessary.
+#' @inheritParams add_array_coords
 #'
 #' @return A \code{tibble}: a copy of \code{sample_info} with additional columns
 #' \code{intra_group_scalar} and \code{group_hires_scalef}

tests/testthat/test-prep_fiji_coords.R

@@ -39,7 +39,7 @@ test_that(
         expect_equal(file.exists(out_file_actual), TRUE)
 
         #   The tissue positions should have the expected columns
-        coords <- readr::read_csv(out_file, show_col_types = FALSE)
+        coords <- readr::read_csv(out_file_expected, show_col_types = FALSE)
         expect_equal(
             colnames(coords),
             c(

tests/testthat/test-prep_fiji_image.R

@@ -40,7 +40,7 @@ test_that(
             file.path(spe_input_dir, "Br2719", "scalefactors_json.json")
         )
         expect_equal(all(file.exists(out_paths_expected)), TRUE)
-        expect_equal(setequal(out_paths_actual, out_paths_expected))
+        expect_equal(setequal(out_paths_actual, out_paths_expected), TRUE)
 
         #   The image should have the correct maximal dimension size
         this_image <- imager::load.image(out_paths_expected[1])