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LieberInstitute · Sep 5, 2024 · 85b0b85 · 85b0b85
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commit 85b0b85
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Showing 10 changed files with 60 additions and 58 deletions.
diff --git a/R/add_array_coords.R b/R/add_array_coords.R
@@ -65,7 +65,7 @@
 #' ########################################################################
 #'
 #' if (file.exists("sample_info.rds")) {
-#'     sample_info <- readRDS('sample_info.rds')
+#'     sample_info <- readRDS("sample_info.rds")
 #' } else {
 #'     sample_info <- dplyr::tibble(
 #'         group = "Br2719",
@@ -80,7 +80,7 @@
 #'     sample_info$spaceranger_dir <- file.path(
 #'         sr_dir, sample_info$capture_area, "outs", "spatial"
 #'     )
-#' 
+#'
 #'     #   Add Fiji-output-related columns
 #'     fiji_dir <- tempdir()
 #'     temp <- unzip(
@@ -89,18 +89,18 @@
 #'     )
 #'     sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
 #'     sample_info$fiji_image_path <- temp[grep("png$", temp)]
-#' 
+#'
 #'     ## Re-size images and add more information to the sample_info
 #'     sample_info <- rescale_fiji_inputs(sample_info, out_dir = tempdir())
-#' 
+#'
 #'     saveRDS(sample_info, "sample_info.rds")
 #' }
 #'
 #' ## Preparing Fiji coordinates and images for build_spe()
 #' spe_input_dir <- tempdir()
 #' prep_fiji_coords(sample_info, out_dir = spe_input_dir)
 #' prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#' 
+#'
 #' ########################################################################
 #' #   Add array coordinates
 #' ########################################################################
@@ -172,9 +172,9 @@ add_array_coords <- function(spe, sample_info, coords_dir, calc_error_metrics =
         coords_list[[i]] <- .fit_to_array(coords, inter_spot_dist_px)
 
         if (calc_error_metrics) {
-            coords_list[[i]] = coords |>
+            coords_list[[i]] <- coords |>
                 mutate(
-                    capture_area = stringr::str_split_i(key, '^[ACTG]+-1_', 2)
+                    capture_area = stringr::str_split_i(key, "^[ACTG]+-1_", 2)
                 ) |>
                 .add_error_metrics(coords_list[[i]], inter_spot_dist_px)
         }

diff --git a/R/array_error_metrics.R b/R/array_error_metrics.R
@@ -12,21 +12,21 @@
 #'
 #' @author Nicholas J. Eagles
 #' @keywords internal
-.get_neighbors = function(i, coords) {
-    this_array_row = coords[[i, 'array_row']]
-    this_array_col = coords[[i, 'array_col']]
-    this_capture_area = coords[[i, 'capture_area']]
+.get_neighbors <- function(i, coords) {
+    this_array_row <- coords[[i, "array_row"]]
+    this_array_col <- coords[[i, "array_col"]]
+    this_capture_area <- coords[[i, "capture_area"]]
 
     #   Grab the keys of the neighboring spots and return
-    neighbor_keys = coords |>
+    neighbor_keys <- coords |>
         filter(
             capture_area == this_capture_area,
             (array_row == this_array_row & array_col == this_array_col - 2) |
-            (array_row == this_array_row & array_col == this_array_col + 2) |
-            (array_row == this_array_row - 1 & array_col == this_array_col - 1) |
-            (array_row == this_array_row - 1 & array_col == this_array_col + 1) |
-            (array_row == this_array_row + 1 & array_col == this_array_col - 1) |
-            (array_row == this_array_row + 1 & array_col == this_array_col + 1)
+                (array_row == this_array_row & array_col == this_array_col + 2) |
+                (array_row == this_array_row - 1 & array_col == this_array_col - 1) |
+                (array_row == this_array_row - 1 & array_col == this_array_col + 1) |
+                (array_row == this_array_row + 1 & array_col == this_array_col - 1) |
+                (array_row == this_array_row + 1 & array_col == this_array_col + 1)
         ) |>
         pull(key)
     return(neighbor_keys)
@@ -52,12 +52,12 @@
 #'
 #' @author Nicholas J. Eagles
 #' @keywords internal
-.get_shared_neighbors = function(coords_new, coords) {
-    coords_new$shared_neighbors = vapply(
+.get_shared_neighbors <- function(coords_new, coords) {
+    coords_new$shared_neighbors <- vapply(
         seq_len(nrow(coords)),
         function(i) {
-            n_before = .get_neighbors(i, coords)
-            n_after = .get_neighbors(i, coords_new)
+            n_before <- .get_neighbors(i, coords)
+            n_after <- .get_neighbors(i, coords_new)
             return(mean(n_before %in% n_after))
         },
         numeric(1)
@@ -70,7 +70,7 @@
 #'
 #' Given `tibble()`s before and after mapping to new array coordinates,
 #' calculate metrics related to the suitability of the mapping.
-#' 
+#'
 #' Add column `shared_neighbors`, the fraction of neighbors a spot started
 #' with that are retained after mapping; add column `euclidean_error`, the
 #' number of multiples of the inter-spot distance a spot must move to be
@@ -91,20 +91,20 @@
 #' and `euclidean_error` columns.
 #'
 #' @importFrom stringr str_split_i
-#' 
+#'
 #' @author Nicholas J. Eagles
 #' @keywords internal
-.add_error_metrics = function(coords, coords_new, inter_spot_dist_px) {
-    coords_new = coords_new |>
+.add_error_metrics <- function(coords, coords_new, inter_spot_dist_px) {
+    coords_new <- coords_new |>
         mutate(
             euclidean_error = (
-                (pxl_col_in_fullres - pxl_col_in_fullres_rounded) ** 2 +
-                (pxl_row_in_fullres - pxl_row_in_fullres_rounded) ** 2
-            ) ** 0.5 / inter_spot_dist_px,
-            capture_area = stringr::str_split_i(key, '^[ACTG]+-1_', 2),
+                (pxl_col_in_fullres - pxl_col_in_fullres_rounded)**2 +
+                    (pxl_row_in_fullres - pxl_row_in_fullres_rounded)**2
+            )**0.5 / inter_spot_dist_px,
+            capture_area = stringr::str_split_i(key, "^[ACTG]+-1_", 2),
         ) |>
         .get_shared_neighbors(coords) |>
         select(-capture_area)
-    
+
     return(coords_new)
 }
diff --git a/R/build_spe.R b/R/build_spe.R
@@ -38,9 +38,9 @@
 #' ########################################################################
 #' #   Prepare sample_info
 #' ########################################################################
-#' 
+#'
 #' if (file.exists("sample_info.rds")) {
-#'     sample_info <- readRDS('sample_info.rds')
+#'     sample_info <- readRDS("sample_info.rds")
 #' } else {
 #'     sample_info <- dplyr::tibble(
 #'         group = "Br2719",
@@ -55,7 +55,7 @@
 #'     sample_info$spaceranger_dir <- file.path(
 #'         sr_dir, sample_info$capture_area, "outs", "spatial"
 #'     )
-#' 
+#'
 #'     #   Add Fiji-output-related columns
 #'     fiji_dir <- tempdir()
 #'     temp <- unzip(
@@ -64,13 +64,13 @@
 #'     )
 #'     sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
 #'     sample_info$fiji_image_path <- temp[grep("png$", temp)]
-#' 
+#'
 #'     ## Re-size images and add more information to the sample_info
 #'     sample_info <- rescale_fiji_inputs(sample_info, out_dir = tempdir())
-#' 
+#'
 #'     saveRDS(sample_info, "sample_info.rds")
 #' }
-#' 
+#'
 #' ## Preparing Fiji coordinates and images for build_spe()
 #' spe_input_dir <- tempdir()
 #' prep_fiji_coords(sample_info, out_dir = spe_input_dir)
@@ -186,7 +186,8 @@ build_spe <- function(sample_info, coords_dir, count_type = "sparse", reference_
     }
 
     spe <- add_array_coords(
-        spe, sample_info, coords_dir, calc_error_metrics = calc_error_metrics
+        spe, sample_info, coords_dir,
+        calc_error_metrics = calc_error_metrics
     )
     spe <- add_overlap_info(spe, "sum_umi")
 

diff --git a/R/prep_fiji_coords.R b/R/prep_fiji_coords.R
@@ -29,7 +29,7 @@
 #'
 #' @examples
 #' if (file.exists("sample_info.rds")) {
-#'     sample_info <- readRDS('sample_info.rds')
+#'     sample_info <- readRDS("sample_info.rds")
 #' } else {
 #'     sample_info <- dplyr::tibble(
 #'         group = "Br2719",
@@ -44,7 +44,7 @@
 #'     sample_info$spaceranger_dir <- file.path(
 #'         sr_dir, sample_info$capture_area, "outs", "spatial"
 #'     )
-#' 
+#'
 #'     #   Add Fiji-output-related columns
 #'     fiji_dir <- tempdir()
 #'     temp <- unzip(
@@ -53,10 +53,10 @@
 #'     )
 #'     sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
 #'     sample_info$fiji_image_path <- temp[grep("png$", temp)]
-#' 
+#'
 #'     ## Re-size images and add more information to the sample_info
 #'     sample_info <- rescale_fiji_inputs(sample_info, out_dir = tempdir())
-#' 
+#'
 #'     saveRDS(sample_info, "sample_info.rds")
 #' }
 #'

diff --git a/R/prep_fiji_image.R b/R/prep_fiji_image.R
@@ -31,7 +31,7 @@
 #'
 #' @examples
 #' if (file.exists("sample_info.rds")) {
-#'     sample_info <- readRDS('sample_info.rds')
+#'     sample_info <- readRDS("sample_info.rds")
 #' } else {
 #'     sample_info <- dplyr::tibble(
 #'         group = "Br2719",
@@ -46,7 +46,7 @@
 #'     sample_info$spaceranger_dir <- file.path(
 #'         sr_dir, sample_info$capture_area, "outs", "spatial"
 #'     )
-#' 
+#'
 #'     #   Add Fiji-output-related columns
 #'     fiji_dir <- tempdir()
 #'     temp <- unzip(
@@ -55,10 +55,10 @@
 #'     )
 #'     sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
 #'     sample_info$fiji_image_path <- temp[grep("png$", temp)]
-#' 
+#'
 #'     ## Re-size images and add more information to the sample_info
 #'     sample_info <- rescale_fiji_inputs(sample_info, out_dir = tempdir())
-#' 
+#'
 #'     saveRDS(sample_info, "sample_info.rds")
 #' }
 #'

diff --git a/R/spe_to_seurat.R b/R/spe_to_seurat.R
@@ -48,15 +48,16 @@
 #'
 #' ## Let's look at our resulting Seurat object
 #' seur_stitched
-spe_to_seurat <- function(spe,
-    spatial_cols = c(
-        "tissue" = "in_tissue",
-        "row" = "array_row",
-        "col" = "array_col",
-        "imagerow" = "pxl_row_in_fullres",
-        "imagecol" = "pxl_col_in_fullres"
-    ),
-    verbose = TRUE) {
+spe_to_seurat <- function(
+        spe,
+        spatial_cols = c(
+            "tissue" = "in_tissue",
+            "row" = "array_row",
+            "col" = "array_col",
+            "imagerow" = "pxl_row_in_fullres",
+            "imagecol" = "pxl_col_in_fullres"
+        ),
+        verbose = TRUE) {
     SPOT_DIAMETER <- 55e-6
 
     #   Ensure all necessary columns are present in colData

diff --git a/tests/testthat/test-add_array_coords.R b/tests/testthat/test-add_array_coords.R
@@ -10,7 +10,7 @@ test_that(
         ########################################################################
 
         if (file.exists("sample_info.rds")) {
-            sample_info <- readRDS('sample_info.rds')
+            sample_info <- readRDS("sample_info.rds")
         } else {
             sample_info <- dplyr::tibble(
                 group = "Br2719",

diff --git a/tests/testthat/test-build_spe.R b/tests/testthat/test-build_spe.R
@@ -15,7 +15,7 @@ test_that(
         ########################################################################
 
         if (file.exists("sample_info.rds")) {
-            sample_info <- readRDS('sample_info.rds')
+            sample_info <- readRDS("sample_info.rds")
         } else {
             sample_info <- dplyr::tibble(
                 group = "Br2719",

diff --git a/tests/testthat/test-prep_fiji_coords.R b/tests/testthat/test-prep_fiji_coords.R
@@ -6,7 +6,7 @@ test_that(
         ########################################################################
 
         if (file.exists("sample_info.rds")) {
-            sample_info <- readRDS('sample_info.rds')
+            sample_info <- readRDS("sample_info.rds")
         } else {
             sample_info <- dplyr::tibble(
                 group = "Br2719",

diff --git a/tests/testthat/test-prep_fiji_image.R b/tests/testthat/test-prep_fiji_image.R
@@ -6,7 +6,7 @@ test_that(
         ########################################################################
 
         if (file.exists("sample_info.rds")) {
-            sample_info <- readRDS('sample_info.rds')
+            sample_info <- readRDS("sample_info.rds")
         } else {
             sample_info <- dplyr::tibble(
                 group = "Br2719",