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LieberInstitute · Jul 26, 2024 · 74c1281 · 74c1281
1 parent 473bcec
commit 74c1281
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Showing 3 changed files with 9 additions and 8 deletions.
diff --git a/R/add_array_coords.R b/R/add_array_coords.R
@@ -188,7 +188,7 @@ add_array_coords <- function(spe, sample_info, coords_dir) {
         cbind(
             coords |>
                 #   Don't add transformed pixel coordinates to colData
-                select(-matches('^pxl_(row|col)_in_fullres$'))
+                select(-matches("^pxl_(row|col)_in_fullres$"))
         ) |>
         S4Vectors::DataFrame()
 

diff --git a/tests/testthat/test-add_array_coords.R b/tests/testthat/test-add_array_coords.R
@@ -55,11 +55,11 @@ test_that(
         expect_identical(spe$array_row, spe_new$array_row_original)
         expect_identical(spe$array_col, spe_new$array_col_original)
         expect_identical(
-            spatialCoords(spe)[, 'pxl_row_in_fullres'],
+            spatialCoords(spe)[, "pxl_row_in_fullres"],
             spe_new$pxl_row_in_fullres_original
         )
         expect_identical(
-            spatialCoords(spe)[, 'pxl_col_in_fullres'],
+            spatialCoords(spe)[, "pxl_col_in_fullres"],
             spe_new$pxl_col_in_fullres_original
         )
     }

diff --git a/vignettes/visiumStitched.Rmd b/vignettes/visiumStitched.Rmd
@@ -135,7 +135,8 @@ with `spatialLIBD::fetch_data()`.
 ## Download example SpaceRanger output files
 sr_dir <- tempdir()
 temp <- unzip(spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
-    exdir = sr_dir)
+    exdir = sr_dir
+)
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -286,7 +287,7 @@ we'll use `spatialLIBD::vis_gene(is_stitched = TRUE)` (version 1.17.8 or newer)
 spatially. For more context on human brain white matter spatial marker genes, check [our previous work on this subject](https://doi.org/10.1038/s41593-020-00787-0).
 
 ```{r "explore_coords", fig.height = 4}
-## Show combined raw expression of white-matter marker genes 
+## Show combined raw expression of white-matter marker genes
 wm_genes <- rownames(spe)[
     match(c("MBP", "GFAP", "PLP1", "AQP4"), rowData(spe)$gene_name)
 ]
@@ -315,8 +316,8 @@ the overlap among capture areas:
 ```{r "array_plot_orig"}
 ## Plot positions of default array coordinates, before overwriting with more
 ## meaningful values. Use custom colors for each capture area
-ca_colors = c("#A33B20", "#e7bb41", "#3d3b8e")
-names(ca_colors) = c("V13B23-283_C1", "V13B23-283_D1", "V13B23-283_A1")
+ca_colors <- c("#A33B20", "#e7bb41", "#3d3b8e")
+names(ca_colors) <- c("V13B23-283_C1", "V13B23-283_D1", "V13B23-283_A1")
 
 colData(spe) |>
     as_tibble() |>
@@ -401,7 +402,7 @@ wm_genes_ens <- rownames(spe_norm)[
     match(c("MBP", "GFAP", "PLP1", "AQP4"), rowData(spe_norm)$gene_name)
 ]
 
-## Plot combination of normalized counts for some white-matter genes 
+## Plot combination of normalized counts for some white-matter genes
 vis_gene(
     spe_norm,
     geneid = wm_genes_ens,