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LieberInstitute · Apr 9, 2024 · 9e4c25a · 9e4c25a
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diff --git a/R/add10xVisiumAnalysis.R b/R/add10xVisiumAnalysis.R
@@ -29,8 +29,9 @@
 #'
 #' ## Note that ?SpatialExperiment::read10xVisium doesn't include all the files
 #' ## we need to illustrate read10xVisiumWrapper().
-add10xVisiumAnalysis <- function(spe,
-    visium_analysis) {
+add10xVisiumAnalysis <- function(
+        spe,
+        visium_analysis) {
     col_info <- colData(spe)
     barcode_present <- "barcode" %in% colnames(col_info)
     if (!barcode_present) {

diff --git a/R/add_images.R b/R/add_images.R
@@ -43,12 +43,13 @@
 #'     ))
 #' }
 add_images <-
-    function(spe,
-    image_dir,
-    image_pattern,
-    image_id_current = "lowres",
-    image_id = image_pattern,
-    image_paths = locate_images(spe, image_dir, image_pattern)) {
+    function(
+        spe,
+        image_dir,
+        image_pattern,
+        image_id_current = "lowres",
+        image_id = image_pattern,
+        image_paths = locate_images(spe, image_dir, image_pattern)) {
         stopifnot(length(names(image_paths)) > 0)
         stopifnot(all(names(image_paths) %in% unique(spe$sample_id)))
         stopifnot(!any(duplicated(names(image_paths))))

diff --git a/R/annotate_registered_clusters.R b/R/annotate_registered_clusters.R
@@ -48,9 +48,10 @@
 #' ## More relaxed merging threshold
 #' annotate_registered_clusters(cor_stats_layer, cutoff_merge_ratio = 1)
 annotate_registered_clusters <-
-    function(cor_stats_layer,
-    confidence_threshold = 0.25,
-    cutoff_merge_ratio = 0.25) {
+    function(
+        cor_stats_layer,
+        confidence_threshold = 0.25,
+        cutoff_merge_ratio = 0.25) {
         annotated <-
             apply(cor_stats_layer,
                 1,
@@ -86,10 +87,11 @@ annotate_registered_clusters <-
     }
 
 annotate_registered_cluster <-
-    function(remaining,
-    label = "",
-    current = NULL,
-    cutoff_merge_ratio = 0.25) {
+    function(
+        remaining,
+        label = "",
+        current = NULL,
+        cutoff_merge_ratio = 0.25) {
         ## Filter negative correlations
         remaining <- remaining[remaining > 0]
 

diff --git a/R/check_sce.R b/R/check_sce.R
@@ -24,40 +24,41 @@
 #'     ## Check the object
 #'     check_sce(sce_example)
 #' }
-check_sce <- function(sce,
-    variables = c(
-        "GraphBased",
-        "ManualAnnotation",
-        "Maynard",
-        "Martinowich",
-        paste0("SNN_k50_k", 4:28),
-        "spatialLIBD",
-        "cell_count",
-        "sum_umi",
-        "sum_gene",
-        "expr_chrM",
-        "expr_chrM_ratio",
-        "SpatialDE_PCA",
-        "SpatialDE_pool_PCA",
-        "HVG_PCA",
-        "pseudobulk_PCA",
-        "markers_PCA",
-        "SpatialDE_UMAP",
-        "SpatialDE_pool_UMAP",
-        "HVG_UMAP",
-        "pseudobulk_UMAP",
-        "markers_UMAP",
-        "SpatialDE_PCA_spatial",
-        "SpatialDE_pool_PCA_spatial",
-        "HVG_PCA_spatial",
-        "pseudobulk_PCA_spatial",
-        "markers_PCA_spatial",
-        "SpatialDE_UMAP_spatial",
-        "SpatialDE_pool_UMAP_spatial",
-        "HVG_UMAP_spatial",
-        "pseudobulk_UMAP_spatial",
-        "markers_UMAP_spatial"
-    )) {
+check_sce <- function(
+        sce,
+        variables = c(
+            "GraphBased",
+            "ManualAnnotation",
+            "Maynard",
+            "Martinowich",
+            paste0("SNN_k50_k", 4:28),
+            "spatialLIBD",
+            "cell_count",
+            "sum_umi",
+            "sum_gene",
+            "expr_chrM",
+            "expr_chrM_ratio",
+            "SpatialDE_PCA",
+            "SpatialDE_pool_PCA",
+            "HVG_PCA",
+            "pseudobulk_PCA",
+            "markers_PCA",
+            "SpatialDE_UMAP",
+            "SpatialDE_pool_UMAP",
+            "HVG_UMAP",
+            "pseudobulk_UMAP",
+            "markers_UMAP",
+            "SpatialDE_PCA_spatial",
+            "SpatialDE_pool_PCA_spatial",
+            "HVG_PCA_spatial",
+            "pseudobulk_PCA_spatial",
+            "markers_PCA_spatial",
+            "SpatialDE_UMAP_spatial",
+            "SpatialDE_pool_UMAP_spatial",
+            "HVG_UMAP_spatial",
+            "pseudobulk_UMAP_spatial",
+            "markers_UMAP_spatial"
+        )) {
     ## Should be a SingleCellExperiment object
     stopifnot(is(sce, "SingleCellExperiment"))
 

diff --git a/R/check_spe.R b/R/check_spe.R
@@ -25,13 +25,14 @@
 #'     ## Check the object
 #'     check_spe(spe)
 #' }
-check_spe <- function(spe,
-    variables = c(
-        "sum_umi",
-        "sum_gene",
-        "expr_chrM",
-        "expr_chrM_ratio"
-    )) {
+check_spe <- function(
+        spe,
+        variables = c(
+            "sum_umi",
+            "sum_gene",
+            "expr_chrM",
+            "expr_chrM_ratio"
+        )) {
     ## Should be a SpatialExperiment object
     stopifnot(is(spe, "SpatialExperiment"))
 

diff --git a/R/fetch_data.R b/R/fetch_data.R
@@ -84,27 +84,26 @@
 #' #> 172.28 MB
 #' }
 fetch_data <-
-    function(
-        type = c(
-            "sce",
-            "sce_layer",
-            "modeling_results",
-            "sce_example",
-            "spe",
-            "spatialDLPFC_Visium",
-            "spatialDLPFC_Visium_example_subset",
-            "spatialDLPFC_Visium_pseudobulk",
-            "spatialDLPFC_Visium_modeling_results",
-            "spatialDLPFC_Visium_SPG",
-            "spatialDLPFC_snRNAseq",
-            "Visium_SPG_AD_Visium_wholegenome_spe",
-            "Visium_SPG_AD_Visium_targeted_spe",
-            "Visium_SPG_AD_Visium_wholegenome_pseudobulk_spe",
-            "Visium_SPG_AD_Visium_wholegenome_modeling_results"
-        ),
-        destdir = tempdir(),
-        eh = ExperimentHub::ExperimentHub(),
-        bfc = BiocFileCache::BiocFileCache()) {
+    function(type = c(
+        "sce",
+        "sce_layer",
+        "modeling_results",
+        "sce_example",
+        "spe",
+        "spatialDLPFC_Visium",
+        "spatialDLPFC_Visium_example_subset",
+        "spatialDLPFC_Visium_pseudobulk",
+        "spatialDLPFC_Visium_modeling_results",
+        "spatialDLPFC_Visium_SPG",
+        "spatialDLPFC_snRNAseq",
+        "Visium_SPG_AD_Visium_wholegenome_spe",
+        "Visium_SPG_AD_Visium_targeted_spe",
+        "Visium_SPG_AD_Visium_wholegenome_pseudobulk_spe",
+        "Visium_SPG_AD_Visium_wholegenome_modeling_results"
+    ),
+    destdir = tempdir(),
+    eh = ExperimentHub::ExperimentHub(),
+    bfc = BiocFileCache::BiocFileCache()) {
         ## Some variables
         sce <-
             sce_layer <- modeling_results <- sce_sub <- spe <- NULL

diff --git a/R/frame_limits.R b/R/frame_limits.R
@@ -37,16 +37,17 @@
 #' }
 #'
 frame_limits <-
-    function(spe,
-    sampleid,
-    image_id = "lowres",
-    visium_grid = list(
-        row_min = 0,
-        row_max = 77,
-        col_min = 0,
-        col_max = 127,
-        fiducial_vs_capture_edge = (8 - 6.5) * 1000 / 2 / 100
-    )) {
+    function(
+        spe,
+        sampleid,
+        image_id = "lowres",
+        visium_grid = list(
+            row_min = 0,
+            row_max = 77,
+            col_min = 0,
+            col_max = 127,
+            fiducial_vs_capture_edge = (8 - 6.5) * 1000 / 2 / 100
+        )) {
         ## Subset the info we need for the particular sample
         d <-
             as.data.frame(cbind(colData(spe), SpatialExperiment::spatialCoords(spe))[spe$sample_id == sampleid, ],

diff --git a/R/gene_set_enrichment.R b/R/gene_set_enrichment.R
@@ -58,11 +58,12 @@
 #' ## Explore the results
 #' asd_sfari_enrichment
 gene_set_enrichment <-
-    function(gene_list,
-    fdr_cut = 0.1,
-    modeling_results = fetch_data(type = "modeling_results"),
-    model_type = names(modeling_results)[1],
-    reverse = FALSE) {
+    function(
+        gene_list,
+        fdr_cut = 0.1,
+        modeling_results = fetch_data(type = "modeling_results"),
+        model_type = names(modeling_results)[1],
+        reverse = FALSE) {
         model_results <- modeling_results[[model_type]]
 
         ## Keep only the genes present

diff --git a/R/gene_set_enrichment_plot.R b/R/gene_set_enrichment_plot.R
@@ -84,17 +84,18 @@
 #'     layerHeights = c(0, 40, 55, 75, 85, 110, 120, 135),
 #' )
 gene_set_enrichment_plot <-
-    function(enrichment,
-    xlabs = unique(enrichment$ID),
-    PThresh = 12,
-    ORcut = 3,
-    enrichOnly = FALSE,
-    layerHeights = c(0, seq_len(length(unique(enrichment$test)))) * 15,
-    mypal = c(
-        "white",
-        grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "YlOrRd"))(50)
-    ),
-    cex = 1.2) {
+    function(
+        enrichment,
+        xlabs = unique(enrichment$ID),
+        PThresh = 12,
+        ORcut = 3,
+        enrichOnly = FALSE,
+        layerHeights = c(0, seq_len(length(unique(enrichment$test)))) * 15,
+        mypal = c(
+            "white",
+            grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "YlOrRd"))(50)
+        ),
+        cex = 1.2) {
         ## Re-order and shorten names if they match our data
         if (all(unique(enrichment$test) %in% c("WM", paste0("Layer", seq_len(6))))) {
             enrichment$test <-

diff --git a/R/geom_spatial.R b/R/geom_spatial.R
@@ -58,14 +58,15 @@
 #'     ## Clean up
 #'     rm(spe_sub)
 #' }
-geom_spatial <- function(mapping = NULL,
-    data = NULL,
-    stat = "identity",
-    position = "identity",
-    na.rm = FALSE,
-    show.legend = NA,
-    inherit.aes = FALSE,
-    ...) {
+geom_spatial <- function(
+        mapping = NULL,
+        data = NULL,
+        stat = "identity",
+        position = "identity",
+        na.rm = FALSE,
+        show.legend = NA,
+        inherit.aes = FALSE,
+        ...) {
     ## To avoid a NOTE on R CMD check
     ggname <- function(prefix, grob) {
         grob$name <- grid::grobName(grob, prefix)

diff --git a/R/img_edit.R b/R/img_edit.R
@@ -58,24 +58,25 @@
 #'     plot(x)
 #' }
 img_edit <-
-    function(spe,
-    sampleid,
-    image_id = "lowres",
-    channel = NA,
-    brightness = 100,
-    saturation = 100,
-    hue = 100,
-    enhance = FALSE,
-    contrast_sharpen = NA,
-    quantize_max = NA,
-    quantize_dither = TRUE,
-    equalize = FALSE,
-    normalize = FALSE,
-    transparent_color = NA,
-    transparent_fuzz = 0,
-    background_color = NA,
-    median_radius = NA,
-    negate = FALSE) {
+    function(
+        spe,
+        sampleid,
+        image_id = "lowres",
+        channel = NA,
+        brightness = 100,
+        saturation = 100,
+        hue = 100,
+        enhance = FALSE,
+        contrast_sharpen = NA,
+        quantize_max = NA,
+        quantize_dither = TRUE,
+        equalize = FALSE,
+        normalize = FALSE,
+        transparent_color = NA,
+        transparent_fuzz = 0,
+        background_color = NA,
+        median_radius = NA,
+        negate = FALSE) {
         img <-
             magick::image_read(SpatialExperiment::imgRaster(spe, sample_id = sampleid, image_id = image_id))
 

diff --git a/R/img_update.R b/R/img_update.R
@@ -41,12 +41,13 @@
 #'     imgData(img_update(spe, sampleid = "151507", brightness = 25))
 #' }
 img_update <-
-    function(spe,
-    sampleid,
-    image_id = "lowres",
-    new_image_id = paste0("edited_", image_id),
-    overwrite = FALSE,
-    ...) {
+    function(
+        spe,
+        sampleid,
+        image_id = "lowres",
+        new_image_id = paste0("edited_", image_id),
+        overwrite = FALSE,
+        ...) {
         img_data <- SpatialExperiment::imgData(spe)
 
         ## Skip this sample if there's no existing image to update

diff --git a/R/img_update_all.R b/R/img_update_all.R
@@ -22,11 +22,12 @@
 #'     imgData(img_update_all(spe, brightness = 25))
 #' }
 img_update_all <-
-    function(spe,
-    image_id = "lowres",
-    new_image_id = paste0("edited_", image_id),
-    overwrite = FALSE,
-    ...) {
+    function(
+        spe,
+        image_id = "lowres",
+        new_image_id = paste0("edited_", image_id),
+        overwrite = FALSE,
+        ...) {
         for (sampleid in unique(spe$sample_id)) {
             spe <-
                 img_update(