fix preprocess

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(aggregate,Matrix)
 export(CellSPA)
 export(calAggExpressionCorrelation)
 export(calBaselineAllMetrics)

R/processing.R

@@ -41,7 +41,8 @@ processingSPE <- function(spe,
     spe <- scater::runUMAP(spe,
                            dimred = "PCA",
                            min_dist = 0.3,
-                           verbose = verbose)
+                           verbose = verbose,
+                           n_neighbors = min(ncol(spe), 15))
     return(spe)
 }
 

R/readMethods.R

@@ -90,6 +90,7 @@ readXenium <- function(data_dir,
 #' corresponding to the meta data in the output files.
 #' @param tiff_path a character specifying the path of a tiff file output from BIDCell.
 #' @param method_name a character specifying the name of the method.
+#' @param spatialCoordsNames a vector of two characters indicate the name of the spatial coordinates for each cell.
 #'
 #' @import SpatialExperiment
 #' @importFrom methods as
@@ -109,9 +110,11 @@ readXenium <- function(data_dir,
 readBIDCell <- function(data_dir,
                         meta_idx = NULL,
                         tiff_path = NULL,
-                        method_name = NULL) {
+                        method_name = NULL,
+                        spatialCoordsNames = c("cell_centroid_x",
+                                               "cell_centroid_y")) {
 
-    all_files <- list.files(data_dir)
+    all_files <- list.files(data_dir, pattern = "csv")
 
     cell_outputs <- lapply(1:length(all_files), function(i) {
         res <- read.csv(file.path(data_dir, all_files[i]))
@@ -155,11 +158,9 @@ readBIDCell <- function(data_dir,
     data <- as(as.matrix(data), "CsparseMatrix")
 
 
-
     spe <- SpatialExperiment(assay = list(counts = Matrix::t(data)),
                              colData = data.frame(meta),
-                             spatialCoordsNames = c("cell_centroid_x",
-                                                    "cell_centroid_y"))
+                             spatialCoordsNames = spatialCoordsNames)
 
     spe <- .initialise_CellSPA_list(spe)
     spe <- .add_dataset_metrics(spe)

R/utils.R

@@ -45,6 +45,7 @@ subset <- function(spe, col_idx) {
 
 # From Matrix.utils::aggregate.Matrix() function, which has been archived on CRAN
 
+#' @export
 aggregate.Matrix <- function(x, groupings = NULL, form = NULL, fun = 'sum', ...) {
     if (!methods::is(x,'Matrix')) {
         x <- Matrix::Matrix(as.matrix(x), sparse = TRUE)

docs/pkgdown.yml

@@ -3,4 +3,4 @@ pkgdown: 2.1.0
 pkgdown_sha: ~
 articles:
   CellSPA: CellSPA.html
-last_built: 2024-09-13T03:13Z
+last_built: 2024-10-15T03:57Z

vignettes/CellSPA.Rmd

@@ -8,27 +8,28 @@ output:
     toc_float: true
 package: BiocStyle
 vignette: >
-  %\VignetteIndexEntry{CellSPA}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
+    %\VignetteIndexEntry{CellSPA}
+    %\VignetteEngine{knitr::rmarkdown}
+    %\VignetteEncoding{UTF-8}
 ---
+
 
 
 ```{r global-options, include=FALSE}
-knitr::opts_chunk$set(
-    message=FALSE,
-    warning=FALSE,
-    collapse=TRUE,
-    comment="#>"
-)
-library(BiocStyle)
+  knitr::opts_chunk$set(
+  message=FALSE,
+  warning=FALSE,
+  collapse=TRUE,
+  comment="#>"
+  )
+  library(BiocStyle)
 ```
-
-
-
-
+  
+  
+  
+  
 ```{r, include=FALSE}
-
+  
 library(CellSPA)
 library(ggplot2)
 library(ggthemes)
@@ -41,14 +42,19 @@ theme_set(theme_bw())
 
 # Read BIDCell output
 
-```{r, cache=TRUE}
+```{r cache = TRUE}
 data_dir <- system.file("extdata/BIDCell_csv_output", package = "CellSPA")
 data_dir
 tiff_path <- system.file("extdata/BIDCell_output_subset.tif", package = "CellSPA")
+spe <- readBIDCell(data_dir,
+                   tiff_path = tiff_path,
+                   method_name = "BIDCell",
+                   spatialCoordsNames = c("cell_centroid_x",
+                                          "cell_centroid_y"))
 ```
 
 
-```{r, cache=TRUE}
+```{r cache = TRUE}
 spe <- processingSPE(spe,
                      qc_range = list(total_transciprts = c(20, 2000),
                                      total_genes = c(20, Inf)))
@@ -82,7 +88,7 @@ head(colData(spe))
 
 ```{r}
 sce_ref_full <- readRDS(system.file("extdata/sce_FFPE_full.rds", 
-                            package = "CellSPA"))
+                                    package = "CellSPA"))
 sce_ref <- processingRef(sce_ref_full, 
                          celltype = sce_ref_full$graph_cluster_anno, 
                          subset_row = rownames(spe))