Rename references of LS to visiumStitched_brain

LieberInstitute · Jul 19, 2024 · 2373930 · 2373930
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commit 2373930
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Showing 21 changed files with 40 additions and 40 deletions.
diff --git a/R/add_array_coords.R b/R/add_array_coords.R
@@ -45,7 +45,7 @@
 #' @author Nicholas J. Eagles
 #'
 #' @examples
-#' spe <- spatialLIBD::fetch_data(type = "Visium_LS_spe")
+#' spe <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
 #' 
 #' ########################################################################
 #' #   Prepare sample_info
@@ -58,7 +58,7 @@
 #' #   Add 'spaceranger_dir' column
 #' sr_dir = tempdir()
 #' temp = unzip(
-#'     spatialLIBD::fetch_data("Visium_LS_spaceranger"), exdir = sr_dir
+#'     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"), exdir = sr_dir
 #' )
 #' sample_info$spaceranger_dir = file.path(
 #'     sr_dir, sample_info$capture_area, 'outs', 'spatial'
@@ -67,7 +67,7 @@
 #' #   Add ImageJ-output-related columns
 #' imagej_dir = tempdir()
 #' temp = unzip(
-#'     spatialLIBD::fetch_data("Visium_LS_ImageJ_out"), exdir = imagej_dir
+#'     spatialLIBD::fetch_data("visiumStitched_brain_ImageJ_out"), exdir = imagej_dir
 #' )
 #' sample_info$imagej_xml_path = temp[grep('xml$', temp)]
 #' sample_info$imagej_image_path = temp[grep('png$', temp)]

diff --git a/R/add_overlap_info.R b/R/add_overlap_info.R
@@ -25,7 +25,7 @@
 #' @author Nicholas J. Eagles
 #'
 #' @examples
-#' spe <- spatialLIBD::fetch_data(type = "Visium_LS_spe")
+#' spe <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
 #' 
 #' #    Find the mean of the 'sum_umi' metric by capture area to understand
 #' #    which capture areas will be excluded in regions of overlap

diff --git a/R/build_spe.R b/R/build_spe.R
@@ -37,7 +37,7 @@
 #' #   Add 'spaceranger_dir' column
 #' sr_dir = tempdir()
 #' temp = unzip(
-#'     spatialLIBD::fetch_data("Visium_LS_spaceranger"), exdir = sr_dir
+#'     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"), exdir = sr_dir
 #' )
 #' sample_info$spaceranger_dir = file.path(
 #'     sr_dir, sample_info$capture_area, 'outs', 'spatial'
@@ -46,7 +46,7 @@
 #' #   Add ImageJ-output-related columns
 #' imagej_dir = tempdir()
 #' temp = unzip(
-#'     spatialLIBD::fetch_data("Visium_LS_ImageJ_out"), exdir = imagej_dir
+#'     spatialLIBD::fetch_data("visiumStitched_brain_ImageJ_out"), exdir = imagej_dir
 #' )
 #' sample_info$imagej_xml_path = temp[grep('xml$', temp)]
 #' sample_info$imagej_image_path = temp[grep('png$', temp)]

diff --git a/R/prep_imagej_coords.R b/R/prep_imagej_coords.R
@@ -33,7 +33,7 @@
 #' #   Add 'spaceranger_dir' column
 #' sr_dir = tempdir()
 #' temp = unzip(
-#'     spatialLIBD::fetch_data("Visium_LS_spaceranger"), exdir = sr_dir
+#'     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"), exdir = sr_dir
 #' )
 #' sample_info$spaceranger_dir = file.path(
 #'     sr_dir, sample_info$capture_area, 'outs', 'spatial'
@@ -42,7 +42,7 @@
 #' #   Add ImageJ-output-related columns
 #' imagej_dir = tempdir()
 #' temp = unzip(
-#'     spatialLIBD::fetch_data("Visium_LS_ImageJ_out"), exdir = imagej_dir
+#'     spatialLIBD::fetch_data("visiumStitched_brain_ImageJ_out"), exdir = imagej_dir
 #' )
 #' sample_info$imagej_xml_path = temp[grep('xml$', temp)]
 #' sample_info$imagej_image_path = temp[grep('png$', temp)]

diff --git a/R/prep_imagej_image.R b/R/prep_imagej_image.R
@@ -34,7 +34,7 @@
 #' #   Add 'spaceranger_dir' column
 #' sr_dir = tempdir()
 #' temp = unzip(
-#'     spatialLIBD::fetch_data("Visium_LS_spaceranger"), exdir = sr_dir
+#'     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"), exdir = sr_dir
 #' )
 #' sample_info$spaceranger_dir = file.path(
 #'     sr_dir, sample_info$capture_area, 'outs', 'spatial'
@@ -43,7 +43,7 @@
 #' #   Add ImageJ-output-related columns
 #' imagej_dir = tempdir()
 #' temp = unzip(
-#'     spatialLIBD::fetch_data("Visium_LS_ImageJ_out"), exdir = imagej_dir
+#'     spatialLIBD::fetch_data("visiumStitched_brain_ImageJ_out"), exdir = imagej_dir
 #' )
 #' sample_info$imagej_xml_path = temp[grep('xml$', temp)]
 #' sample_info$imagej_image_path = temp[grep('png$', temp)]

diff --git a/R/rescale_imagej_inputs.R b/R/rescale_imagej_inputs.R
@@ -41,7 +41,7 @@
 #' #   Add 'spaceranger_dir' column
 #' sr_dir = tempdir()
 #' temp = unzip(
-#'     spatialLIBD::fetch_data("Visium_LS_spaceranger"), exdir = sr_dir
+#'     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"), exdir = sr_dir
 #' )
 #' sample_info$spaceranger_dir = file.path(
 #'     sr_dir, sample_info$capture_area, 'outs', 'spatial'
@@ -50,7 +50,7 @@
 #' #   Add ImageJ-output-related columns
 #' imagej_dir = tempdir()
 #' temp = unzip(
-#'     spatialLIBD::fetch_data("Visium_LS_ImageJ_out"), exdir = imagej_dir
+#'     spatialLIBD::fetch_data("visiumStitched_brain_ImageJ_out"), exdir = imagej_dir
 #' )
 #' sample_info$imagej_xml_path = temp[grep('xml$', temp)]
 #' sample_info$imagej_image_path = temp[grep('png$', temp)]

diff --git a/R/spe_to_seurat.R b/R/spe_to_seurat.R
@@ -21,7 +21,7 @@
 #'
 #' @examples
 #'
-#' spe <- spatialLIBD::fetch_data(type = "Visium_LS_spe")
+#' spe <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
 #'
 #' ## Convert from a SpatialExperiment to a Seurat object
 #' seur <- spe_to_seurat(spe)

diff --git a/man/add_array_coords.Rd b/man/add_array_coords.Rd
diff --git a/man/add_overlap_info.Rd b/man/add_overlap_info.Rd
diff --git a/man/build_spe.Rd b/man/build_spe.Rd
diff --git a/man/prep_imagej_coords.Rd b/man/prep_imagej_coords.Rd
diff --git a/man/prep_imagej_image.Rd b/man/prep_imagej_image.Rd
diff --git a/man/rescale_imagej_inputs.Rd b/man/rescale_imagej_inputs.Rd
diff --git a/man/spe_to_seurat.Rd b/man/spe_to_seurat.Rd
diff --git a/tests/testthat/test-add_array_coords.R b/tests/testthat/test-add_array_coords.R
@@ -1,7 +1,7 @@
 test_that(
     "add_array_coords",
     {
-        spe <- fetch_data(type = "Visium_LS_spe")
+        spe <- fetch_data(type = "visiumStitched_brain_spe")
 
         ########################################################################
         #   Prepare sample_info
@@ -13,14 +13,14 @@ test_that(
         )
         #   Add 'spaceranger_dir' column
         sr_dir = tempdir()
-        temp = unzip(fetch_data("Visium_LS_spaceranger"), exdir = sr_dir)
+        temp = unzip(fetch_data("visiumStitched_brain_spaceranger"), exdir = sr_dir)
         sample_info$spaceranger_dir = file.path(
             sr_dir, sample_info$capture_area, 'outs', 'spatial'
         )
 
         #   Add ImageJ-output-related columns
         imagej_dir = tempdir()
-        temp = unzip(fetch_data("Visium_LS_ImageJ_out"), exdir = imagej_dir)
+        temp = unzip(fetch_data("visiumStitched_brain_ImageJ_out"), exdir = imagej_dir)
         sample_info$imagej_xml_path = temp[grep('xml$', temp)]
         sample_info$imagej_image_path = temp[grep('png$', temp)]
 

diff --git a/tests/testthat/test-add_overlap_info.R b/tests/testthat/test-add_overlap_info.R
@@ -1,7 +1,7 @@
 test_that(
     "add_overlap_info",
     {
-        spe <- fetch_data(type = "Visium_LS_spe")
+        spe <- fetch_data(type = "visiumStitched_brain_spe")
 
         spe$my_metric = 0
         spe$my_metric[spe$capture_area == "V13B23-283_A1"] = 1

diff --git a/tests/testthat/test-build_spe.R b/tests/testthat/test-build_spe.R
@@ -20,14 +20,14 @@ test_that(
         )
         #   Add 'spaceranger_dir' column
         sr_dir = tempdir()
-        temp = unzip(fetch_data("Visium_LS_spaceranger"), exdir = sr_dir)
+        temp = unzip(fetch_data("visiumStitched_brain_spaceranger"), exdir = sr_dir)
         sample_info$spaceranger_dir = file.path(
             sr_dir, sample_info$capture_area, 'outs', 'spatial'
         )
 
         #   Add ImageJ-output-related columns
         imagej_dir = tempdir()
-        temp = unzip(fetch_data("Visium_LS_ImageJ_out"), exdir = imagej_dir)
+        temp = unzip(fetch_data("visiumStitched_brain_ImageJ_out"), exdir = imagej_dir)
         sample_info$imagej_xml_path = temp[grep('xml$', temp)]
         sample_info$imagej_image_path = temp[grep('png$', temp)]
 

diff --git a/tests/testthat/test-prep_imagej_coords.R b/tests/testthat/test-prep_imagej_coords.R
@@ -11,14 +11,14 @@ test_that(
         )
         #   Add 'spaceranger_dir' column
         sr_dir = tempdir()
-        temp = unzip(fetch_data("Visium_LS_spaceranger"), exdir = sr_dir)
+        temp = unzip(fetch_data("visiumStitched_brain_spaceranger"), exdir = sr_dir)
         sample_info$spaceranger_dir = file.path(
             sr_dir, sample_info$capture_area, 'outs', 'spatial'
         )
 
         #   Add ImageJ-output-related columns
         imagej_dir = tempdir()
-        temp = unzip(fetch_data("Visium_LS_ImageJ_out"), exdir = imagej_dir)
+        temp = unzip(fetch_data("visiumStitched_brain_ImageJ_out"), exdir = imagej_dir)
         sample_info$imagej_xml_path = temp[grep('xml$', temp)]
         sample_info$imagej_image_path = temp[grep('png$', temp)]
 

diff --git a/tests/testthat/test-prep_imagej_image.R b/tests/testthat/test-prep_imagej_image.R
@@ -11,14 +11,14 @@ test_that(
         )
         #   Add 'spaceranger_dir' column
         sr_dir = tempdir()
-        temp = unzip(fetch_data("Visium_LS_spaceranger"), exdir = sr_dir)
+        temp = unzip(fetch_data("visiumStitched_brain_spaceranger"), exdir = sr_dir)
         sample_info$spaceranger_dir = file.path(
             sr_dir, sample_info$capture_area, 'outs', 'spatial'
         )
 
         #   Add ImageJ-output-related columns
         imagej_dir = tempdir()
-        temp = unzip(fetch_data("Visium_LS_ImageJ_out"), exdir = imagej_dir)
+        temp = unzip(fetch_data("visiumStitched_brain_ImageJ_out"), exdir = imagej_dir)
         sample_info$imagej_xml_path = temp[grep('xml$', temp)]
         sample_info$imagej_image_path = temp[grep('png$', temp)]
 

diff --git a/tests/testthat/test-rescale_imagej_inputs.R b/tests/testthat/test-rescale_imagej_inputs.R
@@ -11,7 +11,7 @@ test_that(
         )
         #   Add 'spaceranger_dir' column
         sr_dir = tempdir()
-        temp = unzip(fetch_data("Visium_LS_spaceranger"), exdir = sr_dir)
+        temp = unzip(fetch_data("visiumStitched_brain_spaceranger"), exdir = sr_dir)
         sample_info$spaceranger_dir = file.path(
             sr_dir, sample_info$capture_area, 'outs', 'spatial'
         )

diff --git a/vignettes/full_demo.Rmd b/vignettes/full_demo.Rmd
@@ -86,7 +86,7 @@ with `spatialLIBD::fetch_data()`.
 
 ```{r "spaceranger_dir"}
 sr_dir = tempdir()
-temp = unzip(fetch_data("Visium_LS_spaceranger"), exdir = sr_dir)
+temp = unzip(fetch_data("visiumStitched_brain_spaceranger"), exdir = sr_dir)
 sample_info$spaceranger_dir = file.path(
     sr_dir, sample_info$capture_area, 'outs', 'spatial'
 )
@@ -125,7 +125,7 @@ respectively.
 
 ```{r "imagej_out"}
 imagej_dir = tempdir()
-temp = unzip(fetch_data("Visium_LS_ImageJ_out"), exdir = imagej_dir)
+temp = unzip(fetch_data("visiumStitched_brain_ImageJ_out"), exdir = imagej_dir)
 sample_info$imagej_xml_path = temp[grep('xml$', temp)]
 sample_info$imagej_image_path = temp[grep('png$', temp)]
 ```
@@ -288,7 +288,7 @@ object with [normalized](https://bioconductor.org/books/3.12/OSCA/normalization.
 counts from `spatialLIBD`, then plot a few white matter genes as before:
 
 ```{r "fetch_norm"}
-spe_norm = fetch_data(type = 'Visium_LS_spe')
+spe_norm = fetch_data(type = 'visiumStitched_brain_spe')
 
 wm_genes_ens = rownames(spe_norm)[
     match(c("MBP", "GFAP", "PLP1", "AQP4"), rowData(spe_norm)$gene_name)