Merge pull request estellad#1 from estellad/master

All bugs fixed I hope 

Former-commit-id: 68f9ce0
Former-commit-id: 2a95a4add044fae82d29c7bfdb63d278cdee5437

Author: estellad

.DS_Store

@@ -2,6 +2,8 @@
 .Rhistory
 .Rapp.history
 .Rbuildignore
+.DS_Store
+tests/test_realdata_secretely.R
 
 # Session Data files
 .RData

.gitignore

@@ -1,20 +1,35 @@
 Package: SpatialExperimentIO
-Title: Read in Xenium, CosMx, or Merscope data as SpatialExperiment object.
-Version: 0.1.0
+Title: Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object
+Version: 0.0.99
 Authors@R: c(
     person("Yixing E.", "Dong", 
         email = "estelladong729@gmail.com", 
         role = c("aut", "cre"), 
         comment = c(ORCID = "0009-0003-5115-5686")))
 URL: https://github.com/estellad/SpatialExperimentIO
 BugReports: https://github.com/estellad/SpatialExperimentIO/issues
-Description: Read in Xenium, CosMx, or Merscope data as SpatialExperiment object.
-License: MIT
+Description: Read in imaging-based spatial transcriptomics technology data, such as Xenium by 10X Genomics, CosMx by Nanostring, MERSCOPE by Vizgen, or STARmapPLUS from Broad Institute, as a SpatialExperiment or a SingleCellExperiment object. 
+License: MIT + file LICENSE
 Encoding: UTF-8
-LazyData: true
+VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
 Imports: 
   DropletUtils,
   SpatialExperiment,
-  SingleCellExperiment
-RoxygenNote: 7.2.3
+  SingleCellExperiment,
+  methods,
+  utils
+Suggests: 
+  knitr, 
+  rmarkdown, 
+  testthat (>= 3.0.0), 
+  BiocStyle
+biocViews:
+  DataRepresentation, 
+  DataImport, 
+  Infrastructure, 
+  Transcriptomics, 
+  SingleCell, 
+  Spatial
+RoxygenNote: 7.3.1
+Config/testthat/edition: 3

DESCRIPTION

@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2023 Estella Yixing Dong
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2024
+COPYRIGHT HOLDER: Yixing E. Dong

LICENSE

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 Yixing E. Dong
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

LICENSE.md

@@ -6,4 +6,9 @@ export(readStarmapplusSXE)
 export(readXeniumSXE)
 importFrom(DropletUtils,read10xCounts)
 importFrom(SingleCellExperiment,SingleCellExperiment)
+importFrom(SingleCellExperiment,colData)
+importFrom(SingleCellExperiment,counts)
+importFrom(SingleCellExperiment,rowData)
 importFrom(SpatialExperiment,SpatialExperiment)
+importFrom(methods,as)
+importFrom(utils,read.csv)

NAMESPACE

@@ -0,0 +1,3 @@
+# SpatialExperimentIO 0.0.99
+
+* Initial CRAN submission.

NEWS.md

@@ -29,19 +29,19 @@
 #' @return  a \code{\link{SpatialExperiment}} or a \code{\link{SingleCellExperiment}} object 
 #' @export
 #' 
-#' @author Estella Yixing Dong
+#' @author Yixing Estella Dong
 #'
 #' @examples
+#' # A relatively small data download can be from:
 #' \dontrun{
-#' # Data download is from: 
-#' # https://nanostring.com/resources/smi-ffpe-dataset-lung9-rep1-data/
+#' https://nanostring.com/resources/smi-ffpe-dataset-lung9-rep1-data/
+#' }
 #' 
-#' # Here as an example, we have downsized the count matrix and meta data file 
-#' # to only 453 randomly selected cells and 20 genes, and necessary columns 
-#' # of the metadata. 
+#' # A mock counts and mock metadata with spatial location generated for a 8 genes by 
+#' # 9 cells object is in /extdata: 
 #' 
 #' cospath <- system.file(
-#'   file.path("extdata", "NanostringCosMx"),
+#'   file.path("extdata", "CosMx_small"),
 #'   package = "SpatialExperimentIO")
 #'   
 #' list.files(cospath)
@@ -50,56 +50,74 @@
 #' cos_spe <- readCosmxSXE(dirname = cospath)
 #' cos_sce <- readCosmxSXE(dirname = cospath, return_type = "SCE")
 #' 
-#' }
 #' 
 #' @importFrom SpatialExperiment SpatialExperiment
-#' @importFrom SingleCellExperiment SingleCellExperiment
+#' @importFrom SingleCellExperiment SingleCellExperiment rowData counts colData
+#' @importFrom methods as
+#' @importFrom utils read.csv
 readCosmxSXE <- function(dirname = dirname, 
                          return_type = "SPE",
                          countmatfpattern = "exprMat_file.csv", 
                          metadatafpattern = "metadata_file.csv", 
-                         coord_names = c("CenterX_global_px",
-                                         "CenterY_global_px")){
+                         coord_names = c("CenterX_global_px", "CenterY_global_px")){
 
   if(!return_type %in% c("SPE", "SCE")){
     stop("'return_type' must be one of c('SPE', 'SCE')")
   }
 
-  countmat_file <- file.path(dirname, list.files(dirname, countmatfpattern))
+  ## Metadata sanity check 
+  if(!any(file.exists(file.path(dirname, list.files(dirname, metadatafpattern))))){
+    stop("CosMx metadata file does not exist in the directory. Expect 'metadata_file.csv' in `dirname`")
+  }
+  
   metadata_file <- file.path(dirname, list.files(dirname, metadatafpattern))
+  if(length(metadata_file) > 1){
+    stop("More than one metadata file possible with the provided pattern `metadatafpattern`")
+  }
 
+  ## Count matrix sanity check
+  if(!any(file.exists(file.path(dirname, list.files(dirname, countmatfpattern))))){
+    stop("CosMx count matrix does not exist in the directory. Expect 'exprMat_file.csv' in `dirname`")
+  }
+  
+  countmat_file <- file.path(dirname, list.files(dirname, countmatfpattern))
+  if(length(countmat_file) > 1){
+    stop("More than one count matrix file possible with the provided pattern `countmatfpattern`")
+  }
+
   # Read in 
   countmat <- read.csv(countmat_file)
   metadata <- read.csv(metadata_file)
 
   # Count matrix   
-  counts <- merge(countmat, metadata[, c("fov", "cell_ID")])
-  counts <- subset(counts, select = -c(fov, cell_ID))
-  counts <- t(counts)
+  counts_ <- merge(countmat, metadata[, c("fov", "cell_ID")])
+  counts_ <- subset(counts_, select = -c(fov, cell_ID))
+  counts_ <- t(counts_)
 
   # rowData (does not exist)
 
-  # colData
-  colData <- merge(metadata, countmat[, c("fov", "cell_ID")])
+  # metadata
+  metadata <- merge(metadata, countmat[, c("fov", "cell_ID")])
 
+  if(!all(coord_names %in% colnames(metadata))){
+    stop("`coord_names` not in columns of `metadatafpattern`. For CosMx, expect c('CenterX_global_px', 'CenterY_global_px') in the columns of the metadata 'metadata_file.csv'. " )
+  }
 
-  colnames(counts) <- rownames(colData) <- 1:ncol(counts)
+  colnames(counts_) <- rownames(metadata) <- seq_len(ncol(counts_))
 
   if(return_type == "SPE"){
   sxe <- SpatialExperiment::SpatialExperiment(
-    assays = list(counts = counts),
+    assays = list(counts = as(counts_, "dgCMatrix")),
     # rowData = rowData,
-    colData = colData,
+    colData = metadata,
     spatialCoordsNames = coord_names)
   }else if(return_type == "SCE"){
     # construct 'SingleCellExperiment'
     sxe <- SingleCellExperiment::SingleCellExperiment(
-      assays = list(counts = counts),
-      colData = colData
+      assays = list(counts = as(counts_, "dgCMatrix")),
+      colData = metadata
     )
   }
 
-  if(class(counts(sxe)) != "dgCMatrix"){counts(sxe) <- as(counts(sxe), "dgCMatrix")}
-  
   return(sxe)
-}
+}

R/readCosmxSXE.R

@@ -27,21 +27,21 @@
 #' @return  a \code{\link{SpatialExperiment}} or a \code{\link{SingleCellExperiment}} object 
 #' @export
 #' 
-#' @author Estella Yixing Dong
+#' @author Yixing Estella Dong
 #'
 #' @examples
+#' # A relatively small data download can be from:
 #' \dontrun{
-#' # Data download is from: 
 #' https://console.cloud.google.com/storage/browser/vz-ffpe-showcase/
 #' HumanOvarianCancerPatient2Slice2?pageState=(%22StorageObjectListTable%22:
 #' (%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=false
+#' }
 #' 
-#' # Here as an example, we have downsized the count matrix and meta data file to 
-#' # only around 450 randomly selected cells and 20 genes, and necessary columns 
-#' # of the metadata. 
+#' # A mock counts and mock metadata with spatial location generated for a 9 genes by 
+#' # 8 cells object is in /extdata: 
 #' 
 #' merpath <- system.file(
-#'   file.path("extdata", "VizgenMERSCOPE"),
+#'   file.path("extdata", "MERSCOPE_small"),
 #'   package = "SpatialExperimentIO")
 #'   
 #' list.files(merpath)
@@ -50,10 +50,11 @@
 #' mer_spe <- readMerscopeSXE(dirname = merpath)
 #' mer_sce <- readMerscopeSXE(dirname = merpath, return_type = "SCE")
 #' 
-#' }
 #' 
 #' @importFrom SpatialExperiment SpatialExperiment
-#' @importFrom SingleCellExperiment SingleCellExperiment
+#' @importFrom SingleCellExperiment SingleCellExperiment rowData counts colData
+#' @importFrom methods as
+#' @importFrom utils read.csv
 readMerscopeSXE <- function(dirname = dirname, 
                             return_type = "SPE",
                             countmatfpattern = "cell_by_gene.csv", 
@@ -64,8 +65,25 @@ readMerscopeSXE <- function(dirname = dirname,
     stop("'return_type' must be one of c('SPE', 'SCE')")
   }
 
-  countmat_file <- file.path(dirname, list.files(dirname, countmatfpattern))
+  ## Metadata sanity check 
+  if(!any(file.exists(file.path(dirname, list.files(dirname, metadatafpattern))))){
+    stop("MERSCOPE metadata file does not exist in the directory. Expect 'cell_metadata.csv' in `dirname`")
+  }
+  
   metadata_file <- file.path(dirname, list.files(dirname, metadatafpattern))
+  if(length(metadata_file) > 1){
+    stop("More than one metadata file possible with the provided pattern `metadatafpattern`")
+  }
+  
+  ## Count matrix sanity check
+  if(!any(file.exists(file.path(dirname, list.files(dirname, countmatfpattern))))){
+    stop("MERSCOPE count matrix does not exist in the directory. Expect 'cell_by_gene.csv' in `dirname`")
+  }
+  
+  countmat_file <- file.path(dirname, list.files(dirname, countmatfpattern))
+  if(length(countmat_file) > 1){
+    stop("More than one count matrix file possible with the provided pattern `countmatfpattern`")
+  }
 
   # Read in 
   countmat <- read.csv(countmat_file)
@@ -77,31 +95,33 @@ readMerscopeSXE <- function(dirname = dirname,
 
   # Count matrix 
   rownames(countmat) <- countmat$cell + 1 # fix the indexing to start at 1
-  counts <- t(subset(countmat, select = -cell))
+  countmat <- t(subset(countmat, select = -cell))
 
   # rowData (does not exist)
 
-  # colData
+  # metadata
   rownames(metadata) <- metadata$cell + 1
-  colData <- subset(metadata, select = -cell)
+  metadata <- subset(metadata, select = -cell)
+  
+  if(!all(coord_names %in% colnames(metadata))){
+    stop("`coord_names` not in columns of `metadatafpattern`. For MERSCOPE, expect c('center_x', 'center_y') in the columns of the metadata 'cell_metadata.csv'. " )
+  }
 
   if(return_type == "SPE"){
     # construct 'SpatialExperiment'
     sxe <- SpatialExperiment::SpatialExperiment(
-      assays = list(counts = counts),
+      assays = list(counts = as(countmat, "dgCMatrix")),
       # rowData = rowData,
-      colData = colData,
+      colData = metadata,
       spatialCoordsNames = coord_names)
     }else if(return_type == "SCE"){
       # construct 'SingleCellExperiment'
       sxe <- SingleCellExperiment::SingleCellExperiment(
-        assays = list(counts = counts),
-        colData = colData
+        assays = list(counts = as(countmat, "dgCMatrix")),
+        colData = metadata
       )
     }
 
-  if(class(counts(sxe)) != "dgCMatrix"){counts(sxe) <- as(counts(sxe), "dgCMatrix")}
-  
   return(sxe)
 
-}
+}