From 13be60b8b4d8abeb597d4ccee01982d5d5167ee2 Mon Sep 17 00:00:00 2001 From: Mark Keller <7525285+keller-mark@users.noreply.github.com> Date: Mon, 2 Oct 2023 14:09:59 -0400 Subject: [PATCH] Update docs --- NAMESPACE | 1 + R/config.R | 11 ++ R/wrappers.R | 39 ++++ R/wrappers_anndata.R | 77 ++++++-- R/wrappers_csv.R | 47 +++-- man/AbstractWrapper.Rd | 116 +++++++++++ man/{SeuratWrapper.Rd => AnnDataWrapper.Rd} | 96 +++++++-- man/Component.Rd | 4 +- man/CoordinationType.Rd | 4 +- man/CsvWrapper.Rd | 208 ++++++++++++++++++++ man/DataType.Rd | 2 +- man/FileType.Rd | 3 +- man/MultiImageWrapper.Rd | 2 + man/OmeTiffWrapper.Rd | 2 + man/VitessceConfig.Rd | 34 ++-- man/VitessceConfigCoordinationScope.Rd | 2 + man/VitessceConfigDataset.Rd | 14 +- man/VitessceConfigDatasetFile.Rd | 2 + man/VitessceConfigServerRangeRoute.Rd | 84 +++++++- man/export_to_files.Rd | 2 +- man/hconcat.Rd | 4 +- man/vconcat.Rd | 4 +- man/vitessce_widget.Rd | 2 +- vignettes/shiny.Rmd | 17 +- 24 files changed, 692 insertions(+), 85 deletions(-) rename man/{SeuratWrapper.Rd => AnnDataWrapper.Rd} (65%) create mode 100644 man/CsvWrapper.Rd diff --git a/NAMESPACE b/NAMESPACE index 8988f2e..52db099 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,6 +4,7 @@ export(AbstractWrapper) export(AnnDataWrapper) export(Component) export(CoordinationType) +export(CsvWrapper) export(DataType) export(FileType) export(MultiImageWrapper) diff --git a/R/config.R b/R/config.R index f43ebd9..03aa68c 100644 --- a/R/config.R +++ b/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$c_type <- c_type @@ -374,6 +383,7 @@ VitessceConfigView <- R6::R6Class("VitessceConfigView", } invisible(self) }, + #' @description use_coordination_by_dict = function(scopes) { # TODO invisible(self) @@ -429,6 +439,7 @@ VitessceConfig <- R6::R6Class("VitessceConfig", base_dir = NULL, #' @description #' Create a new config object. + #' @param schema_version The Vitessce config schema version to use. #' @param name A name for the config. #' @param description A description for the config. #' @return A new `VitessceConfig` object. diff --git a/R/wrappers.R b/R/wrappers.R index 2da7232..34681aa 100644 --- a/R/wrappers.R +++ b/R/wrappers.R @@ -111,16 +111,42 @@ AbstractWrapper <- R6::R6Class("AbstractWrapper", ) return(route) }, + #' @description + #' Construct a URL to a local directory. + #' + #' @param base_url The base URL on which the web server is serving. + #' @param dataset_uid The ID for this dataset. + #' @param obj_i The index of this data object within the dataset. + #' @param local_dir_path The path to the local directory. + #' @param local_dir_uid A unique identifier for this local directory in this dataset. + #' @return A string for the URL. get_local_dir_url = function(base_url, dataset_uid, obj_i, local_dir_path, local_dir_uid) { if(!self$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$get_route_str(dataset_uid, obj_i, ...)) return(retval) }, + #' @description + #' Construct a URL. + #' @param base_url The base URL on which the web server is serving. + #' @param suffix The suffix to append to the base URL. + #' @return A URL as a string like {base_url}/{suffix} get_url_simple = function(base_url, suffix) { return(paste0(base_url, "/", suffix)) }, diff --git a/R/wrappers_anndata.R b/R/wrappers_anndata.R index a455c37..62bb58c 100644 --- a/R/wrappers_anndata.R +++ b/R/wrappers_anndata.R @@ -1,18 +1,11 @@ -#' Seurat object wrapper class -#' @title SeuratWrapper Class +#' AnnData object wrapper class +#' @title AnnDataWrapper Class #' @docType class #' @description -#' Class representing a local Seurat object in a Vitessce dataset. +#' Class representing an AnnData object (saved to a Zarr store) in a Vitessce dataset. #' -#' @rdname SeuratWrapper +#' @rdname AnnDataWrapper #' @export -#' @examples -#' obj <- get_seurat_obj() -#' w <- SeuratWrapper$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$local_dir_uid)) }, diff --git a/R/wrappers_csv.R b/R/wrappers_csv.R index 67d8bbd..40ab324 100644 --- a/R/wrappers_csv.R +++ b/R/wrappers_csv.R @@ -1,42 +1,46 @@ -#' Seurat object wrapper class -#' @title SeuratWrapper Class +#' CSV file wrapper class +#' @title CsvWrapper Class #' @docType class #' @description -#' Class representing a local Seurat object in a Vitessce dataset. +#' Class representing a CSV file in a Vitessce dataset. #' -#' @rdname SeuratWrapper +#' @rdname CsvWrapper #' @export -#' @examples -#' obj <- get_seurat_obj() -#' w <- SeuratWrapper$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$local_csv_uid)) }, diff --git a/man/AbstractWrapper.Rd b/man/AbstractWrapper.Rd index 6f57f3e..b4d561a 100644 --- a/man/AbstractWrapper.Rd +++ b/man/AbstractWrapper.Rd @@ -37,7 +37,9 @@ Abstract dataset object wrapper class \item \href{#method-AbstractWrapper-get_file_defs}{\code{AbstractWrapper$get_file_defs()}} \item \href{#method-AbstractWrapper-get_out_dir_route}{\code{AbstractWrapper$get_out_dir_route()}} \item \href{#method-AbstractWrapper-get_local_dir_url}{\code{AbstractWrapper$get_local_dir_url()}} +\item \href{#method-AbstractWrapper-get_local_file_url}{\code{AbstractWrapper$get_local_file_url()}} \item \href{#method-AbstractWrapper-get_local_dir_route}{\code{AbstractWrapper$get_local_dir_route()}} +\item \href{#method-AbstractWrapper-get_local_file_route}{\code{AbstractWrapper$get_local_file_route()}} \item \href{#method-AbstractWrapper-get_url}{\code{AbstractWrapper$get_url()}} \item \href{#method-AbstractWrapper-get_url_simple}{\code{AbstractWrapper$get_url_simple()}} \item \href{#method-AbstractWrapper-get_route_str}{\code{AbstractWrapper$get_route_str()}} @@ -151,6 +153,7 @@ A new \code{VitessceConfigServerStaticRoute} instance. \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-AbstractWrapper-get_local_dir_url}{}}} \subsection{Method \code{get_local_dir_url()}}{ +Construct a URL to a local directory. \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AbstractWrapper$get_local_dir_url( base_url, @@ -161,11 +164,64 @@ A new \code{VitessceConfigServerStaticRoute} instance. )}\if{html}{\out{
}} } +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{base_url}}{The base URL on which the web server is serving.} + +\item{\code{dataset_uid}}{The ID for this dataset.} + +\item{\code{obj_i}}{The index of this data object within the dataset.} + +\item{\code{local_dir_path}}{The path to the local directory.} + +\item{\code{local_dir_uid}}{A unique identifier for this local directory in this dataset.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A string for the URL. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AbstractWrapper-get_local_file_url}{}}} +\subsection{Method \code{get_local_file_url()}}{ +Construct a URL to a local file. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{AbstractWrapper$get_local_file_url( + base_url, + dataset_uid, + obj_i, + local_file_path, + local_file_uid +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{base_url}}{The base URL on which the web server is serving.} + +\item{\code{dataset_uid}}{The ID for this dataset.} + +\item{\code{obj_i}}{The index of this data object within the dataset.} + +\item{\code{local_file_path}}{The path to the local file.} + +\item{\code{local_file_uid}}{A unique identifier for this local file in this dataset.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A string for the URL. +} } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-AbstractWrapper-get_local_dir_route}{}}} \subsection{Method \code{get_local_dir_route()}}{ +Create a web server route for this object. \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AbstractWrapper$get_local_dir_route( dataset_uid, @@ -175,6 +231,53 @@ A new \code{VitessceConfigServerStaticRoute} instance. )}\if{html}{\out{
}} } +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{dataset_uid}}{The ID for this dataset.} + +\item{\code{obj_i}}{The index of this data object within the dataset.} + +\item{\code{local_dir_path}}{The path to the local directory.} + +\item{\code{local_dir_uid}}{A unique identifier for this local directory in this dataset.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A new \code{VitessceConfigServerStaticRoute} instance. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AbstractWrapper-get_local_file_route}{}}} +\subsection{Method \code{get_local_file_route()}}{ +Create a web server route for this object. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{AbstractWrapper$get_local_file_route( + dataset_uid, + obj_i, + local_file_path, + local_file_uid +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{dataset_uid}}{The ID for this dataset.} + +\item{\code{obj_i}}{The index of this data object within the dataset.} + +\item{\code{local_file_path}}{The path to the local file.} + +\item{\code{local_file_uid}}{A unique identifier for this local file in this dataset.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A new \code{VitessceConfigServerFileRoute} instance. +} } \if{html}{\out{
}} \if{html}{\out{}} @@ -206,10 +309,23 @@ A URL as a string. \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-AbstractWrapper-get_url_simple}{}}} \subsection{Method \code{get_url_simple()}}{ +Construct a URL. \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AbstractWrapper$get_url_simple(base_url, suffix)}\if{html}{\out{
}} } +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{base_url}}{The base URL on which the web server is serving.} + +\item{\code{suffix}}{The suffix to append to the base URL.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A URL as a string like {base_url}/{suffix} +} } \if{html}{\out{
}} \if{html}{\out{}} diff --git a/man/SeuratWrapper.Rd b/man/AnnDataWrapper.Rd similarity index 65% rename from man/SeuratWrapper.Rd rename to man/AnnDataWrapper.Rd index 139b693..886ffbe 100644 --- a/man/SeuratWrapper.Rd +++ b/man/AnnDataWrapper.Rd @@ -3,20 +3,12 @@ \docType{class} \name{AnnDataWrapper} \alias{AnnDataWrapper} -\title{SeuratWrapper Class} +\title{AnnDataWrapper Class} \description{ -Class representing a local Seurat object in a Vitessce dataset. +Class representing an AnnData object (saved to a Zarr store) in a Vitessce dataset. } \details{ -Seurat object wrapper class -} -\examples{ -obj <- get_seurat_obj() -w <- SeuratWrapper$new( - obj, - cell_embeddings = c("pca"), - cell_embedding_names = c("PCA") -) +AnnData object wrapper class } \keyword{internal} \section{Super class}{ @@ -30,6 +22,40 @@ w <- SeuratWrapper$new( \item{\code{adata_url}}{The object to wrap.} \item{\code{local_dir_uid}}{The path to the local zarr store.} + +\item{\code{obs_feature_matrix_path}}{The path to the observation-by-feature matrix within the Zarr store.} + +\item{\code{feature_filter_path}}{The path to the a column of adata.var within the Zarr store. +Use this if obs_feature_matrix_path points to a subset of adata.X (relative to the full adata.var).} + +\item{\code{initial_feature_filter_path}}{The path to the a column of adata.var within the Zarr store. +Use this to load a subset of the matrix at obs_feature_matrix_path initially.} + +\item{\code{obs_set_paths}}{A list of paths to the observation sets within the Zarr store.} + +\item{\code{obs_set_names}}{A list of names for the observation sets.} + +\item{\code{obs_locations_path}}{The path to the observation locations within the Zarr store.} + +\item{\code{obs_segmentations_path}}{The path to the observation segmentations within the Zarr store.} + +\item{\code{obs_embedding_paths}}{A list of paths to the observation embeddings within the Zarr store.} + +\item{\code{obs_embedding_names}}{A list of names for the observation embeddings.} + +\item{\code{obs_embedding_dims}}{A list of dimensions for the observation embeddings.} + +\item{\code{feature_labels_path}}{The path to the feature labels within the Zarr store.} + +\item{\code{obs_labels_path}}{The path to the observation labels within the Zarr store.} + +\item{\code{obs_labels_paths}}{A list of paths to the observation labels within the Zarr store.} + +\item{\code{obs_labels_names}}{A list of names for the observation labels.} + +\item{\code{coordination_values}}{A list of coordination values for the file definition.} + +\item{\code{request_init}}{A list of requestInit options for the Zarr store.} } \if{html}{\out{}} } @@ -51,6 +77,8 @@ w <- SeuratWrapper$new(
  • vitessceR::AbstractWrapper$get_file_defs()
  • vitessceR::AbstractWrapper$get_local_dir_route()
  • vitessceR::AbstractWrapper$get_local_dir_url()
    • +
  • vitessceR::AbstractWrapper$get_local_file_route()
    • +
  • vitessceR::AbstractWrapper$get_local_file_url()
  • vitessceR::AbstractWrapper$get_out_dir()
  • vitessceR::AbstractWrapper$get_out_dir_route()
  • vitessceR::AbstractWrapper$get_route_str()
    • @@ -94,12 +122,44 @@ Create a wrapper around an AnnData object saved to a Zarr store. \describe{ \item{\code{adata_path}}{The path to a local Zarr store.} +\item{\code{adata_url}}{The URL to a remote Zarr store.} + +\item{\code{obs_feature_matrix_path}}{The path to the observation-by-feature matrix within the Zarr store.} + +\item{\code{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).} + +\item{\code{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.} + +\item{\code{obs_set_paths}}{A list of paths to the observation sets within the Zarr store.} + +\item{\code{obs_set_names}}{A list of names for the observation sets.} + +\item{\code{obs_locations_path}}{The path to the observation locations within the Zarr store.} + +\item{\code{obs_segmentations_path}}{The path to the observation segmentations within the Zarr store.} + +\item{\code{obs_embedding_paths}}{A list of paths to the observation embeddings within the Zarr store.} + +\item{\code{obs_embedding_names}}{A list of names for the observation embeddings.} + +\item{\code{obs_embedding_dims}}{A list of dimensions for the observation embeddings.} + +\item{\code{request_init}}{A list of requestInit options for the Zarr store.} + +\item{\code{feature_labels_path}}{The path to the feature labels within the Zarr store.} + +\item{\code{coordination_values}}{A list of coordination values for the file definition.} + +\item{\code{obs_labels_paths}}{A list of paths to the observation labels within the Zarr store.} + +\item{\code{obs_labels_names}}{A list of names for the observation labels.} + \item{\code{...}}{Parameters inherited from \code{AbstractWrapper}.} } \if{html}{\out{}} } \subsection{Returns}{ -A new \code{SeuratWrapper} object. +A new \code{AnnDataWrapper} object. } } \if{html}{\out{
    }} @@ -117,6 +177,8 @@ Create the JSON output files, web server routes, and file definition creators. \item{\code{dataset_uid}}{The ID for this dataset.} \item{\code{obj_i}}{The index of this data object within the dataset.} + +\item{\code{base_dir}}{A base directory for local data.} } \if{html}{\out{}} } @@ -125,10 +187,20 @@ Create the JSON output files, web server routes, and file definition creators. \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-AnnDataWrapper-make_routes}{}}} \subsection{Method \code{make_routes()}}{ +Get a list of server route objects. \subsection{Usage}{ \if{html}{\out{
    }}\preformatted{AnnDataWrapper$make_routes(dataset_uid, obj_i)}\if{html}{\out{
    }} } +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{dataset_uid}}{The ID for this dataset.} + +\item{\code{obj_i}}{The index of this data object within the dataset.} +} +\if{html}{\out{
    }} +} } \if{html}{\out{
    }} \if{html}{\out{}} diff --git a/man/Component.Rd b/man/Component.Rd index 36ce25e..2b6f396 100644 --- a/man/Component.Rd +++ b/man/Component.Rd @@ -5,7 +5,7 @@ \alias{Component} \title{Enumeration of Component values} \format{ -An object of class \code{list} of length 10. +An object of class \code{list} of length 12. } \usage{ Component @@ -26,7 +26,7 @@ valid string constant values representing components. } } \examples{ -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") dataset <- vc$add_dataset("My dataset") description <- vc$add_view(dataset, Component$DESCRIPTION) vc$layout(description) diff --git a/man/CoordinationType.Rd b/man/CoordinationType.Rd index 9619756..bc6716b 100644 --- a/man/CoordinationType.Rd +++ b/man/CoordinationType.Rd @@ -5,7 +5,7 @@ \alias{CoordinationType} \title{Enumeration of Coordination Type values} \format{ -An object of class \code{list} of length 34. +An object of class \code{list} of length 35. } \usage{ CoordinationType @@ -50,7 +50,7 @@ in the coordination space. } } \examples{ -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ref_dataset <- vc$add_dataset("Reference") qry_dataset <- vc$add_dataset("Query") ref_plot <- vc$add_view(ref_dataset, Component$SCATTERPLOT, mapping = "umap") diff --git a/man/CsvWrapper.Rd b/man/CsvWrapper.Rd new file mode 100644 index 0000000..d28c90f --- /dev/null +++ b/man/CsvWrapper.Rd @@ -0,0 +1,208 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/wrappers_csv.R +\docType{class} +\name{CsvWrapper} +\alias{CsvWrapper} +\title{CsvWrapper Class} +\description{ +Class representing a CSV file in a Vitessce dataset. +} +\details{ +CSV file wrapper class +} +\keyword{internal} +\section{Super class}{ +\code{\link[vitessceR:AbstractWrapper]{vitessceR::AbstractWrapper}} -> \code{CsvWrapper} +} +\section{Public fields}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{csv_path}}{The object to wrap.} + +\item{\code{csv_url}}{The object to wrap.} + +\item{\code{local_csv_uid}}{The path to the local zarr store.} + +\item{\code{data_type}}{The Vitessce data type for this file.} + +\item{\code{options}}{A list of options to pass to the Vitessce file definition.} + +\item{\code{coordination_values}}{A list of coordination values to pass to the Vitessce file definition.} + +\item{\code{request_init}}{A list of requestInit values to pass to fetch when loading the CSV over HTTP.} +} +\if{html}{\out{
    }} +} +\section{Methods}{ +\subsection{Public methods}{ +\itemize{ +\item \href{#method-CsvWrapper-new}{\code{CsvWrapper$new()}} +\item \href{#method-CsvWrapper-convert_and_save}{\code{CsvWrapper$convert_and_save()}} +\item \href{#method-CsvWrapper-make_routes}{\code{CsvWrapper$make_routes()}} +\item \href{#method-CsvWrapper-get_csv_url}{\code{CsvWrapper$get_csv_url()}} +\item \href{#method-CsvWrapper-make_file_def_creator}{\code{CsvWrapper$make_file_def_creator()}} +\item \href{#method-CsvWrapper-clone}{\code{CsvWrapper$clone()}} +} +} +\if{html}{\out{ +
    Inherited methods + +
    +}} +\if{html}{\out{
    }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-CsvWrapper-new}{}}} +\subsection{Method \code{new()}}{ +Create a wrapper around a CSV file. +\subsection{Usage}{ +\if{html}{\out{
    }}\preformatted{CsvWrapper$new( + csv_path = NA, + csv_url = NA, + data_type = NA, + options = NA, + coordination_values = NA, + request_init = NA, + ... +)}\if{html}{\out{
    }} +} + +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{csv_path}}{The path to a local CSV file.} + +\item{\code{csv_url}}{The URL to a remote CSV file.} + +\item{\code{data_type}}{The Vitessce data type for this file.} + +\item{\code{options}}{A list of options to pass to the Vitessce file definition.} + +\item{\code{coordination_values}}{A list of coordination values to pass to the Vitessce file definition.} + +\item{\code{request_init}}{A list of requestInit values to pass to fetch when loading the CSV over HTTP.} + +\item{\code{...}}{Parameters inherited from \code{AbstractWrapper}.} +} +\if{html}{\out{
    }} +} +\subsection{Returns}{ +A new \code{CsvWrapper} object. +} +} +\if{html}{\out{
    }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-CsvWrapper-convert_and_save}{}}} +\subsection{Method \code{convert_and_save()}}{ +Create the JSON output files, web server routes, and file definition creators. +\subsection{Usage}{ +\if{html}{\out{
    }}\preformatted{CsvWrapper$convert_and_save(dataset_uid, obj_i, base_dir = NA)}\if{html}{\out{
    }} +} + +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{dataset_uid}}{The ID for this dataset.} + +\item{\code{obj_i}}{The index of this data object within the dataset.} + +\item{\code{base_dir}}{A base directory for local data.} +} +\if{html}{\out{
    }} +} +} +\if{html}{\out{
    }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-CsvWrapper-make_routes}{}}} +\subsection{Method \code{make_routes()}}{ +Get a list of server route objects. +\subsection{Usage}{ +\if{html}{\out{
    }}\preformatted{CsvWrapper$make_routes(dataset_uid, obj_i)}\if{html}{\out{
    }} +} + +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{dataset_uid}}{The ID for this dataset.} + +\item{\code{obj_i}}{The index of this data object within the dataset.} +} +\if{html}{\out{
    }} +} +} +\if{html}{\out{
    }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-CsvWrapper-get_csv_url}{}}} +\subsection{Method \code{get_csv_url()}}{ +Get the URL to the Zarr store, to fill in the file URL in the file definitions. +\subsection{Usage}{ +\if{html}{\out{
    }}\preformatted{CsvWrapper$get_csv_url(base_url, dataset_uid, obj_i)}\if{html}{\out{
    }} +} + +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{base_url}}{The base URL, on which the route will be served.} + +\item{\code{dataset_uid}}{The ID for this dataset.} + +\item{\code{obj_i}}{The index of this data object within the dataset.} +} +\if{html}{\out{
    }} +} +\subsection{Returns}{ +A URL as a string. +} +} +\if{html}{\out{
    }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-CsvWrapper-make_file_def_creator}{}}} +\subsection{Method \code{make_file_def_creator()}}{ +Make the file definition creator function for the cells data type. +\subsection{Usage}{ +\if{html}{\out{
    }}\preformatted{CsvWrapper$make_file_def_creator(dataset_uid, obj_i)}\if{html}{\out{
    }} +} + +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{dataset_uid}}{The ID for this dataset.} + +\item{\code{obj_i}}{The index of this data object within the dataset.} +} +\if{html}{\out{
    }} +} +\subsection{Returns}{ +A file definition creator function which takes a \code{base_url} parameter. +} +} +\if{html}{\out{
    }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-CsvWrapper-clone}{}}} +\subsection{Method \code{clone()}}{ +The objects of this class are cloneable with this method. +\subsection{Usage}{ +\if{html}{\out{
    }}\preformatted{CsvWrapper$clone(deep = FALSE)}\if{html}{\out{
    }} +} + +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{deep}}{Whether to make a deep clone.} +} +\if{html}{\out{
    }} +} +} +} diff --git a/man/DataType.Rd b/man/DataType.Rd index a5be5e9..0e94a6b 100644 --- a/man/DataType.Rd +++ b/man/DataType.Rd @@ -25,7 +25,7 @@ for dataset files. } \examples{ base_url <- "http://localhost:8000/" -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") dataset <- vc$add_dataset("My dataset")$add_file( url = paste0(base_url, "cells.json"), data_type = DataType$CELLS, diff --git a/man/FileType.Rd b/man/FileType.Rd index c5810d3..1989981 100644 --- a/man/FileType.Rd +++ b/man/FileType.Rd @@ -26,10 +26,9 @@ for dataset files. } \examples{ base_url <- "http://localhost:8000/" -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") dataset <- vc$add_dataset("My dataset")$add_file( url = paste0(base_url, "cells.json"), - data_type = DataType$CELLS, file_type = FileType$CELLS_JSON ) } diff --git a/man/MultiImageWrapper.Rd b/man/MultiImageWrapper.Rd index 64a65f0..c39b129 100644 --- a/man/MultiImageWrapper.Rd +++ b/man/MultiImageWrapper.Rd @@ -40,6 +40,8 @@ Image wrapper class
  • vitessceR::AbstractWrapper$get_file_defs()
  • vitessceR::AbstractWrapper$get_local_dir_route()
  • vitessceR::AbstractWrapper$get_local_dir_url()
    • +
  • vitessceR::AbstractWrapper$get_local_file_route()
    • +
  • vitessceR::AbstractWrapper$get_local_file_url()
  • vitessceR::AbstractWrapper$get_out_dir()
  • vitessceR::AbstractWrapper$get_out_dir_route()
  • vitessceR::AbstractWrapper$get_route_str()
    • diff --git a/man/OmeTiffWrapper.Rd b/man/OmeTiffWrapper.Rd index 3a8bf3e..fbf71ce 100644 --- a/man/OmeTiffWrapper.Rd +++ b/man/OmeTiffWrapper.Rd @@ -52,6 +52,8 @@ this image (see http://www.opengl-tutorial.org/beginners-tutorials/tutorial-3-ma
  • vitessceR::AbstractWrapper$get_file_defs()
  • vitessceR::AbstractWrapper$get_local_dir_route()
  • vitessceR::AbstractWrapper$get_local_dir_url()
    • +
  • vitessceR::AbstractWrapper$get_local_file_route()
    • +
  • vitessceR::AbstractWrapper$get_local_file_url()
  • vitessceR::AbstractWrapper$get_out_dir()
  • vitessceR::AbstractWrapper$get_out_dir_route()
  • vitessceR::AbstractWrapper$get_route_str()
    • diff --git a/man/VitessceConfig.Rd b/man/VitessceConfig.Rd index 6642e5c..9dbcaf0 100644 --- a/man/VitessceConfig.Rd +++ b/man/VitessceConfig.Rd @@ -16,14 +16,14 @@ VitessceConfig ## Method `VitessceConfig$add_dataset` ## ------------------------------------------------ -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ds <- vc$add_dataset("My dataset") ## ------------------------------------------------ ## Method `VitessceConfig$add_view` ## ------------------------------------------------ -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ds <- vc$add_dataset("My dataset") spatial <- vc$add_view(ds, "spatial") @@ -31,7 +31,7 @@ spatial <- vc$add_view(ds, "spatial") ## Method `VitessceConfig$add_coordination` ## ------------------------------------------------ -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ds <- vc$add_dataset("My dataset") spatial <- vc$add_view(ds, "spatial") c_scopes <- vc$add_coordination(c("spatialZoom", "spatialTargetX")) @@ -41,7 +41,7 @@ spatial$use_coordination(c_scopes) ## Method `VitessceConfig$layout` ## ------------------------------------------------ -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ds <- vc$add_dataset("My dataset") spatial <- vc$add_view(ds, "spatial") scatterplot <- vc$add_view(ds, "scatterplot") @@ -50,7 +50,7 @@ scatterplot <- vc$add_view(ds, "scatterplot") ## Method `VitessceConfig$link_views` ## ------------------------------------------------ -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ref_dataset <- vc$add_dataset("Reference") qry_dataset <- vc$add_dataset("Query") ref_plot <- vc$add_view(ref_dataset, Component$SCATTERPLOT, mapping = "umap") @@ -65,7 +65,7 @@ vc$link_views( ## Method `VitessceConfig$to_list` ## ------------------------------------------------ -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ds <- vc$add_dataset("My dataset") vc_list <- vc$to_list(base_url = "http://localhost:8000") @@ -73,7 +73,7 @@ vc_list <- vc$to_list(base_url = "http://localhost:8000") ## Method `VitessceConfig$widget` ## ------------------------------------------------ -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") dataset <- vc$add_dataset("My dataset") description <- vc$add_view(dataset, Component$DESCRIPTION) vc$layout(description) @@ -83,7 +83,7 @@ vc$widget() ## Method `VitessceConfig$export` ## ------------------------------------------------ -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") dataset <- vc$add_dataset("My dataset") description <- vc$add_view(dataset, Component$DESCRIPTION) vc$layout(description) @@ -129,6 +129,8 @@ Create a new config object. \subsection{Arguments}{ \if{html}{\out{
    }} \describe{ +\item{\code{schema_version}}{The Vitessce config schema version to use.} + \item{\code{name}}{A name for the config.} \item{\code{description}}{A description for the config.} @@ -162,7 +164,7 @@ A new \code{VitessceConfigDataset} object. } \subsection{Examples}{ \if{html}{\out{
    }} -\preformatted{vc <- VitessceConfig$new("My config") +\preformatted{vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ds <- vc$add_dataset("My dataset") } \if{html}{\out{
    }} @@ -211,7 +213,7 @@ A new \code{VitessceConfigView} object. } \subsection{Examples}{ \if{html}{\out{
    }} -\preformatted{vc <- VitessceConfig$new("My config") +\preformatted{vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ds <- vc$add_dataset("My dataset") spatial <- vc$add_view(ds, "spatial") } @@ -241,7 +243,7 @@ A list of new \code{VitessceConfigCoordinationScope} objects. } \subsection{Examples}{ \if{html}{\out{
    }} -\preformatted{vc <- VitessceConfig$new("My config") +\preformatted{vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ds <- vc$add_dataset("My dataset") spatial <- vc$add_view(ds, "spatial") c_scopes <- vc$add_coordination(c("spatialZoom", "spatialTargetX")) @@ -300,7 +302,7 @@ Self, to allow chaining. } \subsection{Examples}{ \if{html}{\out{
    }} -\preformatted{vc <- VitessceConfig$new("My config") +\preformatted{vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ds <- vc$add_dataset("My dataset") spatial <- vc$add_view(ds, "spatial") scatterplot <- vc$add_view(ds, "scatterplot") @@ -341,7 +343,7 @@ Self, to allow chaining. } \subsection{Examples}{ \if{html}{\out{
    }} -\preformatted{vc <- VitessceConfig$new("My config") +\preformatted{vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ref_dataset <- vc$add_dataset("Reference") qry_dataset <- vc$add_dataset("Query") ref_plot <- vc$add_view(ref_dataset, Component$SCATTERPLOT, mapping = "umap") @@ -378,7 +380,7 @@ A \code{list} that can be serialized to JSON. } \subsection{Examples}{ \if{html}{\out{
    }} -\preformatted{vc <- VitessceConfig$new("My config") +\preformatted{vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ds <- vc$add_dataset("My dataset") vc_list <- vc$to_list(base_url = "http://localhost:8000") } @@ -437,7 +439,7 @@ The Vitessce htmlwidget. } \subsection{Examples}{ \if{html}{\out{
    }} -\preformatted{vc <- VitessceConfig$new("My config") +\preformatted{vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") dataset <- vc$add_dataset("My dataset") description <- vc$add_view(dataset, Component$DESCRIPTION) vc$layout(description) @@ -475,7 +477,7 @@ The Vitessce configuration as a list, with the \code{base_url} filled in. } \subsection{Examples}{ \if{html}{\out{
    }} -\preformatted{vc <- VitessceConfig$new("My config") +\preformatted{vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") dataset <- vc$add_dataset("My dataset") description <- vc$add_view(dataset, Component$DESCRIPTION) vc$layout(description) diff --git a/man/VitessceConfigCoordinationScope.Rd b/man/VitessceConfigCoordinationScope.Rd index 00def26..cb7d30a 100644 --- a/man/VitessceConfigCoordinationScope.Rd +++ b/man/VitessceConfigCoordinationScope.Rd @@ -45,6 +45,8 @@ Create a new coordination scope object. \item{\code{c_type}}{A coordination type name.} \item{\code{c_scope}}{A coordination scope name.} + +\item{\code{c_value}}{An initial value for the coordination scope.} } \if{html}{\out{
    }} } diff --git a/man/VitessceConfigDataset.Rd b/man/VitessceConfigDataset.Rd index 884a4d0..5a44219 100644 --- a/man/VitessceConfigDataset.Rd +++ b/man/VitessceConfigDataset.Rd @@ -17,7 +17,7 @@ Dataset in a VitessceConfig ## ------------------------------------------------ base_url <- "http://localhost:8000/" -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") dataset <- vc$add_dataset("My dataset")$add_file( url = paste0(base_url, "cells.json"), data_type = DataType$CELLS, @@ -61,6 +61,8 @@ Create a new dataset object. \item{\code{uid}}{A unique identifier string for the dataset.} \item{\code{name}}{A name for the dataset} + +\item{\code{base_dir}}{A directory which local files are configured relative to.} } \if{html}{\out{
    }} } @@ -72,19 +74,27 @@ A new \code{VitessceConfigDataset} object. \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-VitessceConfigDataset-get_name}{}}} \subsection{Method \code{get_name()}}{ +Get the dataset name. \subsection{Usage}{ \if{html}{\out{
    }}\preformatted{VitessceConfigDataset$get_name()}\if{html}{\out{
    }} } +\subsection{Returns}{ +The name as a string. +} } \if{html}{\out{
    }} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-VitessceConfigDataset-get_uid}{}}} \subsection{Method \code{get_uid()}}{ +Get the dataset UID. \subsection{Usage}{ \if{html}{\out{
    }}\preformatted{VitessceConfigDataset$get_uid()}\if{html}{\out{
    }} } +\subsection{Returns}{ +The uid as a string. +} } \if{html}{\out{
    }} \if{html}{\out{}} @@ -120,7 +130,7 @@ Invisible self, to allow chaining. \subsection{Examples}{ \if{html}{\out{
    }} \preformatted{base_url <- "http://localhost:8000/" -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") dataset <- vc$add_dataset("My dataset")$add_file( url = paste0(base_url, "cells.json"), data_type = DataType$CELLS, diff --git a/man/VitessceConfigDatasetFile.Rd b/man/VitessceConfigDatasetFile.Rd index ab42ed0..7c28c50 100644 --- a/man/VitessceConfigDatasetFile.Rd +++ b/man/VitessceConfigDatasetFile.Rd @@ -42,6 +42,8 @@ Create a new dataset file object. \item{\code{options}}{A list of options to include for the file.} +\item{\code{coordination_values}}{A list of coordination values to include in the file definition.} + \item{\code{data_type}}{A data type for the file.} } \if{html}{\out{
    }} diff --git a/man/VitessceConfigServerRangeRoute.Rd b/man/VitessceConfigServerRangeRoute.Rd index 1a68d77..b023a08 100644 --- a/man/VitessceConfigServerRangeRoute.Rd +++ b/man/VitessceConfigServerRangeRoute.Rd @@ -1,11 +1,16 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/server.R -\name{VitessceConfigServerRangeRoute} +\name{VitessceConfigServerFileRoute} +\alias{VitessceConfigServerFileRoute} \alias{VitessceConfigServerRangeRoute} \title{Class representing a local web server route for a file which needs to support range requests.} \description{ Class representing a local web server route for a file which needs to support range requests. +Class representing a local web server route for a file which needs to support range requests. + +Class representing a local web server route for a file which needs to support range requests. + Class representing a local web server route for a file which needs to support range requests. } \keyword{internal} @@ -14,6 +19,83 @@ Class representing a local web server route for a file which needs to support ra \describe{ \item{\code{path}}{The path on which the web server should respond to requests using this callback.} +\item{\code{file_path}}{The file to serve.} +} +\if{html}{\out{
    }} +} +\section{Methods}{ +\subsection{Public methods}{ +\itemize{ +\item \href{#method-VitessceConfigServerFileRoute-new}{\code{VitessceConfigServerFileRoute$new()}} +\item \href{#method-VitessceConfigServerFileRoute-create_handlers}{\code{VitessceConfigServerFileRoute$create_handlers()}} +\item \href{#method-VitessceConfigServerFileRoute-clone}{\code{VitessceConfigServerFileRoute$clone()}} +} +} +\if{html}{\out{
    }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-VitessceConfigServerFileRoute-new}{}}} +\subsection{Method \code{new()}}{ +Create a new server route wrapper object. +\subsection{Usage}{ +\if{html}{\out{
    }}\preformatted{VitessceConfigServerFileRoute$new(path, file_path)}\if{html}{\out{
    }} +} + +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{path}}{The route path.} + +\item{\code{file_path}}{The file to serve on this route.} +} +\if{html}{\out{
    }} +} +\subsection{Returns}{ +A new \code{VitessceConfigServerRangeRoute} object. +} +} +\if{html}{\out{
    }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-VitessceConfigServerFileRoute-create_handlers}{}}} +\subsection{Method \code{create_handlers()}}{ +Add handler functions to the Plumber server object to respond on this route. +\subsection{Usage}{ +\if{html}{\out{
    }}\preformatted{VitessceConfigServerFileRoute$create_handlers(pr_server)}\if{html}{\out{
    }} +} + +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{pr_server}}{The server instance.} +} +\if{html}{\out{
    }} +} +\subsection{Returns}{ +The modified server instance. +} +} +\if{html}{\out{
    }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-VitessceConfigServerFileRoute-clone}{}}} +\subsection{Method \code{clone()}}{ +The objects of this class are cloneable with this method. +\subsection{Usage}{ +\if{html}{\out{
    }}\preformatted{VitessceConfigServerFileRoute$clone(deep = FALSE)}\if{html}{\out{
    }} +} + +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{deep}}{Whether to make a deep clone.} +} +\if{html}{\out{
    }} +} +} +} +\section{Public fields}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{path}}{The path on which the web server should respond to requests using this callback.} + \item{\code{file_path}}{The file to serve.} } \if{html}{\out{
    }} diff --git a/man/export_to_files.Rd b/man/export_to_files.Rd index 2f157fb..99adbfa 100644 --- a/man/export_to_files.Rd +++ b/man/export_to_files.Rd @@ -23,7 +23,7 @@ A helper function to export files associated with a particular Vitessce configur We do not recommend calling this function directly. Instead, use the \code{export()} function on a \code{VitessceConfig} instance. } \examples{ -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") dataset <- vc$add_dataset("My dataset") description <- vc$add_view(dataset, Component$DESCRIPTION) vc$layout(description) diff --git a/man/hconcat.Rd b/man/hconcat.Rd index b3011e8..e1e3ede 100644 --- a/man/hconcat.Rd +++ b/man/hconcat.Rd @@ -16,10 +16,10 @@ A \code{VitessceConfigViewHConcat} object. A helper function to construct a new \code{VitessceConfigViewHConcat} object based on multiple views. } \examples{ -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ds <- vc$add_dataset("My dataset") spatial <- vc$add_view(ds, Component$SPATIAL) -gene_list <- vc$add_view(ds, Component$GENES) +gene_list <- vc$add_view(ds, Component$FEATURE_LIST) vc$layout(hconcat(spatial, gene_list)) vc$widget() } diff --git a/man/vconcat.Rd b/man/vconcat.Rd index fede6f8..609438c 100644 --- a/man/vconcat.Rd +++ b/man/vconcat.Rd @@ -16,10 +16,10 @@ A \code{VitessceConfigViewVConcat} object. A helper function to construct a new \code{VitessceConfigViewVConcat} object based on multiple views. } \examples{ -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") ds <- vc$add_dataset("My dataset") spatial <- vc$add_view(ds, Component$SPATIAL) -gene_list <- vc$add_view(ds, Component$GENES) +gene_list <- vc$add_view(ds, Component$FEATURE_LIST) vc$layout(vconcat(spatial, gene_list)) vc$widget() } diff --git a/man/vitessce_widget.Rd b/man/vitessce_widget.Rd index 7a61965..0ec9ac0 100644 --- a/man/vitessce_widget.Rd +++ b/man/vitessce_widget.Rd @@ -49,6 +49,6 @@ recommend calling the \code{widget()} method on the \code{VitessceConfig} instance. } \examples{ -vc <- VitessceConfig$new("My config") +vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config") vc$widget() } diff --git a/vignettes/shiny.Rmd b/vignettes/shiny.Rmd index 3b3bbc9..f536662 100644 --- a/vignettes/shiny.Rmd +++ b/vignettes/shiny.Rmd @@ -14,6 +14,7 @@ First, install the dependencies: install.packages("shiny") install.packages("devtools") devtools::install_github("satijalab/seurat-data") +devtools::install_github("vitessce/vitessceAnalysisR") ``` Next, create an output element in the UI with `vitessce_output` and a corresponding server response with `render_vitessce`. @@ -23,17 +24,21 @@ The value for the `output_id` parameter in the `vitessce_output` function should ```r library(shiny) library(vitessceR) +library(vitessceAnalysisR) library(SeuratData) SeuratData::InstallData("pbmc3k") data("pbmc3k.final") force(pbmc3k.final) -w <- SeuratWrapper$new( - pbmc3k.final, - cell_embeddings = c("pca", "umap"), - cell_embedding_names = c("PCA", "UMAP"), - cell_set_metas = c("seurat_annotations", "seurat_clusters") +adata_path <- file.path("data", "seurat", "pbmc3k.final.h5ad.zarr") +vitessceAnalysisR::seurat_to_anndata_zarr(pbmc3k.final, adata_path) + +w <- AnnDataWrapper$new( + adata_path=adata_path, + obs_embedding_paths = c("obsm/X_pca", "obsm/X_umap"), + obs_embedding_names = c("PCA", "UMAP"), + obs_set_paths = c("obs/seurat_annotations", "obs/seurat_clusters") ) ui <- fluidPage( @@ -48,7 +53,7 @@ server <- function(input, output, session) { dataset <- dataset$add_object(w) scatterplot <- vc$add_view(dataset, Component$SCATTERPLOT, mapping = "PCA") vc$layout(scatterplot) - vc$widget() + vc$widget(theme="light") }) }