Update docs

NAMESPACE

@@ -4,6 +4,7 @@ export(AbstractWrapper)
 export(AnnDataWrapper)
 export(Component)
 export(CoordinationType)
+export(CsvWrapper)
 export(DataType)
 export(FileType)
 export(MultiImageWrapper)

R/config.R

@@ -60,6 +60,7 @@ VitessceConfigDatasetFile <- R6::R6Class("VitessceConfigDatasetFile",
     #' @param data_type A data type for the file.
     #' @param file_type A file type for the file.
     #' @param options A list of options to include for the file.
+    #' @param coordination_values A list of coordination values to include in the file definition.
     #' @return A new `VitessceConfigDatasetFile` object.
     initialize = function(url = NA, file_type = NA, options = NA, coordination_values = NA, data_type = NA) {
       private$file <- obj_list()
@@ -103,6 +104,7 @@ VitessceConfigDataset <- R6::R6Class("VitessceConfigDataset",
     #' Create a new dataset object.
     #' @param uid A unique identifier string for the dataset.
     #' @param name A name for the dataset
+    #' @param base_dir A directory which local files are configured relative to.
     #' @return A new `VitessceConfigDataset` object.
     initialize = function(uid, name, base_dir = NA) {
       self$dataset <- list(
@@ -113,9 +115,15 @@ VitessceConfigDataset <- R6::R6Class("VitessceConfigDataset",
       private$objs <- list()
       self$base_dir <- base_dir
     },
+    #' @description
+    #' Get the dataset name.
+    #' @return The name as a string.
     get_name = function() {
       return(self$dataset[['name']])
     },
+    #' @description
+    #' Get the dataset UID.
+    #' @return The uid as a string.
     get_uid = function() {
       return(self$dataset[['uid']])
     },
@@ -231,6 +239,7 @@ VitessceConfigCoordinationScope <- R6::R6Class("VitessceConfigCoordinationScope"
     #' Create a new coordination scope object.
     #' @param c_type A coordination type name.
     #' @param c_scope A coordination scope name.
+    #' @param c_value An initial value for the coordination scope.
     #' @return A new `VitessceConfigCoordinationScope` object.
     initialize = function(c_type, c_scope, c_value = NA) {
       self$c_type <- c_type
@@ -374,6 +383,7 @@ VitessceConfigView <- R6::R6Class("VitessceConfigView",
       }
       invisible(self)
     },
+    #' @description
     use_coordination_by_dict = function(scopes) {
       # TODO
       invisible(self)
@@ -429,6 +439,7 @@ VitessceConfig <- R6::R6Class("VitessceConfig",
     base_dir = NULL,
     #' @description
     #' Create a new config object.
+    #' @param schema_version The Vitessce config schema version to use.
     #' @param name A name for the config.
     #' @param description A description for the config.
     #' @return A new `VitessceConfig` object.

R/wrappers.R

@@ -111,16 +111,42 @@ AbstractWrapper <- R6::R6Class("AbstractWrapper",
       )
       return(route)
     },
+    #' @description
+    #' Construct a URL to a local directory.
+    #'
+    #' @param base_url The base URL on which the web server is serving.
+    #' @param dataset_uid The ID for this dataset.
+    #' @param obj_i The index of this data object within the dataset.
+    #' @param local_dir_path The path to the local directory.
+    #' @param local_dir_uid A unique identifier for this local directory in this dataset.
+    #' @return A string for the URL.
     get_local_dir_url = function(base_url, dataset_uid, obj_i, local_dir_path, local_dir_uid) {
       if(!self$is_remote && !is.na(self$base_dir)) {
         return(self$get_url_simple(base_url, file_path_to_url_path(local_dir_path, prepend_slash = FALSE)))
       }
       return(self$get_url(base_url, dataset_uid, obj_i, local_dir_uid))
     },
+    #' @description
+    #' Construct a URL to a local file.
+    #'
+    #' @param base_url The base URL on which the web server is serving.
+    #' @param dataset_uid The ID for this dataset.
+    #' @param obj_i The index of this data object within the dataset.
+    #' @param local_file_path The path to the local file.
+    #' @param local_file_uid A unique identifier for this local file in this dataset.
+    #' @return A string for the URL.
     get_local_file_url = function(base_url, dataset_uid, obj_i, local_file_path, local_file_uid) {
       # Same logic as get_local_dir_url
       return(self$get_local_dir_url(base_url, dataset_uid, obj_i, local_file_path, local_file_uid))
     },
+    #' @description
+    #' Create a web server route for this object.
+    #'
+    #' @param dataset_uid The ID for this dataset.
+    #' @param obj_i The index of this data object within the dataset.
+    #' @param local_dir_path The path to the local directory.
+    #' @param local_dir_uid A unique identifier for this local directory in this dataset.
+    #' @return A new `VitessceConfigServerStaticRoute` instance.
     get_local_dir_route = function(dataset_uid, obj_i, local_dir_path, local_dir_uid) {
       if(!self$is_remote) {
         if(is.na(self$base_dir)) {
@@ -137,6 +163,14 @@ AbstractWrapper <- R6::R6Class("AbstractWrapper",
       }
       return(list())
     },
+    #' @description
+    #' Create a web server route for this object.
+    #'
+    #' @param dataset_uid The ID for this dataset.
+    #' @param obj_i The index of this data object within the dataset.
+    #' @param local_file_path The path to the local file.
+    #' @param local_file_uid A unique identifier for this local file in this dataset.
+    #' @return A new `VitessceConfigServerFileRoute` instance.
     get_local_file_route = function(dataset_uid, obj_i, local_file_path, local_file_uid) {
       if(!self$is_remote) {
         if(is.na(self$base_dir)) {
@@ -166,6 +200,11 @@ AbstractWrapper <- R6::R6Class("AbstractWrapper",
         retval <- paste0(base_url, self$get_route_str(dataset_uid, obj_i, ...))
         return(retval)
     },
+    #' @description
+    #' Construct a URL.
+    #' @param base_url The base URL on which the web server is serving.
+    #' @param suffix The suffix to append to the base URL.
+    #' @return A URL as a string like {base_url}/{suffix}
     get_url_simple = function(base_url, suffix) {
       return(paste0(base_url, "/", suffix))
     },

R/wrappers_anndata.R

@@ -1,18 +1,11 @@
-#' Seurat object wrapper class
-#' @title SeuratWrapper Class
+#' AnnData object wrapper class
+#' @title AnnDataWrapper Class
 #' @docType class
 #' @description
-#' Class representing a local Seurat object in a Vitessce dataset.
+#' Class representing an AnnData object (saved to a Zarr store) in a Vitessce dataset.
 #'
-#' @rdname SeuratWrapper
+#' @rdname AnnDataWrapper
 #' @export
-#' @examples
-#' obj <- get_seurat_obj()
-#' w <- SeuratWrapper$new(
-#'   obj,
-#'   cell_embeddings = c("pca"),
-#'   cell_embedding_names = c("PCA")
-#' )
 AnnDataWrapper <- R6::R6Class("AnnDataWrapper",
   inherit = AbstractWrapper,
   public = list(
@@ -25,30 +18,77 @@ AnnDataWrapper <- R6::R6Class("AnnDataWrapper",
     #' @field local_dir_uid The path to the local zarr store.
     #' @keywords internal
     local_dir_uid = NULL,
-
-
+    #' @field obs_feature_matrix_path The path to the observation-by-feature matrix within the Zarr store.
+    #' @keywords internal
     obs_feature_matrix_path=NULL,
+    #' @field feature_filter_path The path to the a column of adata.var within the Zarr store.
+    #' Use this if obs_feature_matrix_path points to a subset of adata.X (relative to the full adata.var).
+    #' @keywords internal
     feature_filter_path=NULL,
+    #' @field initial_feature_filter_path The path to the a column of adata.var within the Zarr store.
+    #' Use this to load a subset of the matrix at obs_feature_matrix_path initially.
+    #' @keywords internal
     initial_feature_filter_path=NULL,
+    #' @field obs_set_paths A list of paths to the observation sets within the Zarr store.
+    #' @keywords internal
     obs_set_paths=NULL,
+    #' @field obs_set_names A list of names for the observation sets.
+    #' @keywords internal
     obs_set_names=NULL,
+    #' @field obs_locations_path The path to the observation locations within the Zarr store.
+    #' @keywords internal
     obs_locations_path=NULL,
+    #' @field obs_segmentations_path The path to the observation segmentations within the Zarr store.
+    #' @keywords internal
     obs_segmentations_path=NULL,
+    #' @field obs_embedding_paths A list of paths to the observation embeddings within the Zarr store.
+    #' @keywords internal
     obs_embedding_paths=NULL,
+    #' @field obs_embedding_names A list of names for the observation embeddings.
+    #' @keywords internal
     obs_embedding_names=NULL,
+    #' @field obs_embedding_dims A list of dimensions for the observation embeddings.
+    #' @keywords internal
     obs_embedding_dims=NULL,
-    request_init=NULL,
+    #' @field feature_labels_path The path to the feature labels within the Zarr store.
+    #' @keywords internal
     feature_labels_path=NULL,
+    #' @field obs_labels_path The path to the observation labels within the Zarr store.
+    #' @keywords internal
     obs_labels_path=NULL,
+    #' @field obs_labels_paths A list of paths to the observation labels within the Zarr store.
+    #' @keywords internal
     obs_labels_paths=NULL,
+    #' @field obs_labels_names A list of names for the observation labels.
+    #' @keywords internal
     obs_labels_names=NULL,
+    #' @field coordination_values A list of coordination values for the file definition.
+    #' @keywords internal
     coordination_values=NULL,
-
+    #' @field request_init A list of requestInit options for the Zarr store.
+    #' @keywords internal
+    request_init=NULL,
     #' @description
     #' Create a wrapper around an AnnData object saved to a Zarr store.
     #' @param adata_path The path to a local Zarr store.
+    #' @param adata_url The URL to a remote Zarr store.
+    #' @param obs_feature_matrix_path The path to the observation-by-feature matrix within the Zarr store.
+    #' @param feature_filter_path The path to the a column of adata.var within the Zarr store. Use this if obs_feature_matrix_path points to a subset of adata.X (relative to the full adata.var).
+    #' @param initial_feature_filter_path The path to the a column of adata.var within the Zarr store. Use this to load a subset of the matrix at obs_feature_matrix_path initially.
+    #' @param obs_set_paths A list of paths to the observation sets within the Zarr store.
+    #' @param obs_set_names A list of names for the observation sets.
+    #' @param obs_locations_path The path to the observation locations within the Zarr store.
+    #' @param obs_segmentations_path The path to the observation segmentations within the Zarr store.
+    #' @param obs_embedding_paths A list of paths to the observation embeddings within the Zarr store.
+    #' @param obs_embedding_names A list of names for the observation embeddings.
+    #' @param obs_embedding_dims A list of dimensions for the observation embeddings.
+    #' @param request_init A list of requestInit options for the Zarr store.
+    #' @param feature_labels_path The path to the feature labels within the Zarr store.
+    #' @param obs_labels_paths A list of paths to the observation labels within the Zarr store.
+    #' @param obs_labels_names A list of names for the observation labels.
+    #' @param coordination_values A list of coordination values for the file definition.
     #' @param ... Parameters inherited from `AbstractWrapper`.
-    #' @return A new `SeuratWrapper` object.
+    #' @return A new `AnnDataWrapper` object.
     initialize = function(adata_path = NA, adata_url = NA, obs_feature_matrix_path = NA, feature_filter_path = NA, initial_feature_filter_path = NA, obs_set_paths = NA, obs_set_names = NA, obs_locations_path = NA, obs_segmentations_path = NA, obs_embedding_paths = NA, obs_embedding_names = NA, obs_embedding_dims = NA, request_init = NA, feature_labels_path = NA, obs_labels_path = NA, coordination_values = NA, obs_labels_paths = NA, obs_labels_names = NA, ...) {
       super$initialize(...)
       self$adata_path <- adata_path
@@ -91,6 +131,7 @@ AnnDataWrapper <- R6::R6Class("AnnDataWrapper",
     #' Create the JSON output files, web server routes, and file definition creators.
     #' @param dataset_uid The ID for this dataset.
     #' @param obj_i The index of this data object within the dataset.
+    #' @param base_dir A base directory for local data.
     convert_and_save = function(dataset_uid, obj_i, base_dir = NA) {
       if(self$is_remote) {
         super$convert_and_save(dataset_uid, obj_i, base_dir = base_dir)
@@ -108,6 +149,10 @@ AnnDataWrapper <- R6::R6Class("AnnDataWrapper",
         self$routes <- append(self$routes, route)
       }
     },
+    #' @description
+    #' Get a list of server route objects.
+    #' @param dataset_uid The ID for this dataset.
+    #' @param obj_i The index of this data object within the dataset.
     make_routes = function(dataset_uid, obj_i) {
       return(self$get_local_dir_route(dataset_uid, obj_i, self$adata_path, self$local_dir_uid))
     },

R/wrappers_csv.R

@@ -1,42 +1,46 @@
-#' Seurat object wrapper class
-#' @title SeuratWrapper Class
+#' CSV file wrapper class
+#' @title CsvWrapper Class
 #' @docType class
 #' @description
-#' Class representing a local Seurat object in a Vitessce dataset.
+#' Class representing a CSV file in a Vitessce dataset.
 #'
-#' @rdname SeuratWrapper
+#' @rdname CsvWrapper
 #' @export
-#' @examples
-#' obj <- get_seurat_obj()
-#' w <- SeuratWrapper$new(
-#'   obj,
-#'   cell_embeddings = c("pca"),
-#'   cell_embedding_names = c("PCA")
-#' )
 CsvWrapper <- R6::R6Class("CsvWrapper",
   inherit = AbstractWrapper,
   public = list(
-    #' @field adata_path The object to wrap.
+    #' @field csv_path The object to wrap.
     #' @keywords internal
     csv_path = NULL,
-    #' @field adata_url The object to wrap.
+    #' @field csv_url The object to wrap.
     #' @keywords internal
     csv_url = NULL,
-    #' @field local_dir_uid The path to the local zarr store.
+    #' @field local_csv_uid The path to the local zarr store.
     #' @keywords internal
     local_csv_uid = NULL,
 
-
+    #' @field data_type The Vitessce data type for this file.
+    #' @keywords internal
     data_type = NULL,
+    #' @field options A list of options to pass to the Vitessce file definition.
+    #' @keywords internal
     options=NULL,
+    #' @field coordination_values A list of coordination values to pass to the Vitessce file definition.
+    #' @keywords internal
     coordination_values=NULL,
+    #' @field request_init A list of requestInit values to pass to fetch when loading the CSV over HTTP.
+    #' @keywords internal
     request_init = NULL,
-
     #' @description
-    #' Create a wrapper around an AnnData object saved to a Zarr store.
-    #' @param adata_path The path to a local Zarr store.
+    #' Create a wrapper around a CSV file.
+    #' @param csv_path The path to a local CSV file.
+    #' @param csv_url The URL to a remote CSV file.
+    #' @param data_type The Vitessce data type for this file.
+    #' @param options A list of options to pass to the Vitessce file definition.
+    #' @param coordination_values A list of coordination values to pass to the Vitessce file definition.
+    #' @param request_init A list of requestInit values to pass to fetch when loading the CSV over HTTP.
     #' @param ... Parameters inherited from `AbstractWrapper`.
-    #' @return A new `SeuratWrapper` object.
+    #' @return A new `CsvWrapper` object.
     initialize = function(csv_path = NA, csv_url = NA, data_type = NA, options = NA, coordination_values = NA, request_init = NA, ...) {
       super$initialize(...)
       self$csv_path <- csv_path
@@ -71,6 +75,7 @@ CsvWrapper <- R6::R6Class("CsvWrapper",
     #' Create the JSON output files, web server routes, and file definition creators.
     #' @param dataset_uid The ID for this dataset.
     #' @param obj_i The index of this data object within the dataset.
+    #' @param base_dir A base directory for local data.
     convert_and_save = function(dataset_uid, obj_i, base_dir = NA) {
       if(self$is_remote) {
         super$convert_and_save(dataset_uid, obj_i, base_dir = base_dir)
@@ -88,6 +93,10 @@ CsvWrapper <- R6::R6Class("CsvWrapper",
         self$routes <- append(self$routes, route)
       }
     },
+    #' @description
+    #' Get a list of server route objects.
+    #' @param dataset_uid The ID for this dataset.
+    #' @param obj_i The index of this data object within the dataset.
     make_routes = function(dataset_uid, obj_i) {
       return(self$get_local_file_route(dataset_uid, obj_i, self$csv_path, self$local_csv_uid))
     },