Run devtools::document() and make read10xVisiumWrapper internally depend on spe_add_info()

Author: Nick-Eagles

R/read10xVisiumWrapper.R

@@ -19,6 +19,8 @@
 #' @param gtf_cols A `character()` specifying which columns to keep from the GTF
 #' file. `"gene_name"` and `"gene_id"` have to be included in `gtf_cols`.
 #' @param verbose A `logical(1)` specifying whether to show progress updates.
+#' @param add_analysis A `logical(1)` specifying whether to read and add
+#' SpaceRanger analysis results.
 #'
 #' @return A [SpatialExperiment][SpatialExperiment-class] object with the
 #' clustering and dimension reduction (projection) results from SpaceRanger by
@@ -53,34 +55,11 @@ read10xVisiumWrapper <- function(samples = "",
     reference_gtf = NULL,
     chrM = "chrM",
     gtf_cols = c("source", "type", "gene_id", "gene_version", "gene_name", "gene_type"),
-    verbose = TRUE) {
-    stopifnot(all(c("gene_name", "gene_id") %in% gtf_cols))
-
-    if (missing(reference_gtf)) {
-        summary_file <- file.path(samples[1], "web_summary.html")
-        web <- readLines(summary_file)
-
-        #   For spaceranger versions before 3.0
-        reference_path <- gsub('.*"', "", regmatches(web, regexpr('\\["Reference Path", *"[/|A-z|0-9|-]+', web)))
-
-        #   For recent spaceranger versions (3.0.0+?)
-        if (length(reference_path) == 0) {
-            reference_path <- sub(
-                ".*--transcriptome=(\\S*).*",
-                "\\1",
-                web[grep("--transcriptome=", web)]
-            )
-        }
-        reference_gtf <- list.files(
-            file.path(reference_path, "genes"), "^genes\\.gtf(\\.gz)?$",
-            full.names = TRUE
-        )
-    }
-    reference_gtf <- reference_gtf[file.exists(reference_gtf)]
-    if (length(reference_gtf) > 1) {
-        stop("More than one 'reference_gtf' was provided or detected. Manually specify the path to just one 'reference_gtf'. If different GTF files were used, then different genes will have been quantified and thus cannot be merged naively into a single SpatialExperiment object. If that's the case, we recommend you build separate SPE objects based on the different 'reference_gtf' files used.", call. = FALSE)
-    } else if (length(reference_gtf) == 0) {
-        stop("No 'reference_gtf' files were detected. Please check that the files are available.", call. = FALSE)
+    verbose = TRUE,
+    add_analysis = TRUE
+    ) {
+    if (!all(c("gene_name", "gene_id") %in% gtf_cols)) {
+        stop("'gtf_cols' must include 'gene_name' and 'gene_id'", call. = FALSE)
     }
 
     if (verbose) message(Sys.time(), " SpatialExperiment::read10xVisium: reading basic data from SpaceRanger")
@@ -93,56 +72,17 @@ read10xVisiumWrapper <- function(samples = "",
         load = load
     )
 
-    if (verbose) message(Sys.time(), " read10xVisiumAnalysis: reading analysis output from SpaceRanger")
-    visium_analysis <- read10xVisiumAnalysis(
+    spe <- spe_add_info(
+        spe = spe,
         samples = samples,
-        sample_id = sample_id
+        sample_id = sample_id,
+        reference_gtf = reference_gtf,
+        chrM = chrM,
+        gtf_cols = gtf_cols,
+        add_analysis = add_analysis,
+        verbose = verbose
     )
 
-    if (verbose) message(Sys.time(), " add10xVisiumAnalysis: adding analysis output from SpaceRanger")
-    spe <- add10xVisiumAnalysis(spe, visium_analysis)
-
-    ## Read in the gene information from the annotation GTF file
-    if (verbose) message(Sys.time(), " rtracklayer::import: reading the reference GTF file")
-    gtf <- rtracklayer::import(reference_gtf)
-    gtf <- gtf[gtf$type == "gene"]
-    names(gtf) <- gtf$gene_id
-
-    ## Match the genes
-    if (verbose) message(Sys.time(), " adding gene information to the SPE object")
-    match_genes <- match(rownames(spe), gtf$gene_id)
-
-    if (all(is.na(match_genes))) {
-        ## Protect against scenario where one set has GENCODE IDs and the other one has ENSEMBL IDs.
-        warning("Gene IDs did not match. This typically happens when you are not using the same GTF file as the one that was used by SpaceRanger. For example, one file uses GENCODE IDs and the other one ENSEMBL IDs. read10xVisiumWrapper() will try to convert them to ENSEMBL IDs.", call. = FALSE)
-        match_genes <- match(gsub("\\..*", "", rownames(spe)), gsub("\\..*", "", gtf$gene_id))
-    }
-
-    if (any(is.na(match_genes))) {
-        warning("Dropping ", sum(is.na(match_genes)), " out of ", length(match_genes), " genes for which we don't have information on the reference GTF file. This typically happens when you are not using the same GTF file as the one that was used by SpaceRanger.", call. = FALSE)
-        ## Drop the few genes for which we don't have information
-        spe <- spe[!is.na(match_genes), ]
-        match_genes <- match_genes[!is.na(match_genes)]
-    }
-
-    ## Keep only some columns from the gtf
-    mcols(gtf) <- mcols(gtf)[, gtf_cols[gtf_cols %in% colnames(mcols(gtf))]]
-
-    ## Add the gene info to our SPE object
-    rowRanges(spe) <- gtf[match_genes]
-
-    ## Add information used by spatialLIBD
-    if (verbose) message(Sys.time(), " adding information used by spatialLIBD")
-    spe <- add_key(spe)
-    spe$sum_umi <- colSums(counts(spe))
-    spe$sum_gene <- colSums(counts(spe) > 0)
-    rowData(spe)$gene_search <- paste0(rowData(spe)$gene_name, "; ", rowData(spe)$gene_id)
-    is_mito <- which(seqnames(spe) == chrM)
-    spe$expr_chrM <- colSums(counts(spe)[is_mito, , drop = FALSE])
-    spe$expr_chrM_ratio <- spe$expr_chrM / spe$sum_umi
-    ## Add a variable for saving the manual annotations
-    spe$ManualAnnotation <- "NA"
-
     ## Done!
     return(spe)
 }

R/spe_add_info.R

@@ -8,6 +8,10 @@
 #' @param spe A [SpatialExperiment-class][SpatialExperiment::SpatialExperiment-class]
 #' object, such as one created by initially running `VisiumIO::TENxVisium()` or
 #' `VisiumIO::TENxVisiumHD()`.
+#' 
+#' @return A [SpatialExperiment-class][SpatialExperiment::SpatialExperiment-class]
+#' object with gene info, SpaceRanger analysis results, and other information
+#' attached.
 spe_add_info <- function(
         spe,
         samples,