add examples

SydneyBioX · Jul 13, 2023 · b780c7c · b780c7c
1 parent 5e9321d
commit b780c7c
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Showing 12 changed files with 72 additions and 2 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -3,3 +3,4 @@
 docs
 ^.*\.md$
 ^data-raw$
+TODO.md
diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,5 @@ vignettes/data
 .DS_Store
 ^.*\.md$
 ^data-raw$
+TODO.md
+data-raw
diff --git a/R/readMethods.R b/R/readMethods.R
@@ -19,6 +19,14 @@
 #' @importFrom SummarizedExperiment rowData
 #'
 #' @return A SpatialExperiment object
+#' @examples
+#'
+#' tenX_output_dir <- system.file("extdata/10x_output_subset", package = "CellSPA")
+#' tenX_output_tif <- system.file("extdata/10x_output_subset/10x_from_csv_subset.tif",
+#'                                 package = "CellSPA")
+#' spe_10x <- readXenium(tenX_output_dir,
+#'                       tiff_path = tenX_output_tif)
+#'
 #' @export
 
 
@@ -87,6 +95,14 @@ readXenium <- function(data_dir,
 #' @importFrom methods as
 #' @importFrom Matrix t
 #' @return A SpatialExperiment object
+#' @examples
+#'
+#' data_dir <- system.file("extdata/BIDCell_csv_output", package = "CellSPA")
+#' tiff_path <- system.file("extdata/BIDCell_output_subset.tif", package = "CellSPA")
+#' spe <- readBIDCell(data_dir,
+#'                    tiff_path = tiff_path,
+#'                    method_name = "BIDCell")
+#'
 #' @export
 
 
@@ -177,6 +193,9 @@ readBIDCell <- function(data_dir,
 #' @importFrom tiff readTIFF
 #' @importFrom reshape2 melt
 #' @return A SpatialExperiment object
+#'
+#' tiff_path <- system.file("extdata/BIDCell_output_subset.tif", package = "CellSPA")
+#' tiff_res <- readTiffOutput(tiff_path = tiff_path)
 #' @export
 
 readTiffOutput <- function(tiff_path) {

diff --git a/docs/articles/CellSPA.html b/docs/articles/CellSPA.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.6
 pkgdown_sha: ~
 articles:
   CellSPA: CellSPA.html
-last_built: 2023-07-13T18:23Z
+last_built: 2023-07-13T20:28Z
 
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
diff --git a/docs/reference/readBIDCell.html b/docs/reference/readBIDCell.html
diff --git a/docs/reference/readTiffOutput.html b/docs/reference/readTiffOutput.html
diff --git a/docs/reference/readXenium.html b/docs/reference/readXenium.html
diff --git a/man/readBIDCell.Rd b/man/readBIDCell.Rd
diff --git a/man/readTiffOutput.Rd b/man/readTiffOutput.Rd
diff --git a/man/readXenium.Rd b/man/readXenium.Rd