R/constants.R
In vitessce/vitessce-r: Create Interactive Single-cell Visualizations with the 'Vitessce' JavaScript Library
#' Enumeration of Coordination Type values
#'
#' The \code{CoordinationType} list contains an enumeration of
#' valid string constant values representing coordination types
#' in the coordination space.
#' \itemize{
#' \item `DATASET`: The dataset to be used for a view.
#' \item `EMBEDDING_TYPE`: The type of embedding to be used in the embedding scatterplot view, for example "UMAP" or "t-SNE".
#' \item `EMBEDDING_ZOOM`: The zoom level of an embedding scatterplot view.
#' \item `EMBEDDING_ROTATION`: The rotation of an embedding scatterplot view.
#' \item `EMBEDDING_TARGET_X`: The x-axis center of an embedding scatterplot view.
#' \item `EMBEDDING_TARGET_Y`: The y-axis center of an embedding scatterplot view.
#' \item `EMBEDDING_TARGET_Z`: The z-axis center of an embedding scatterplot view.
#' \item `SPATIAL_ZOOM`: The zoom level of a spatial view.
#' \item `SPATIAL_ROTATION`: The rotation of a spatial view.
#' \item `SPATIAL_TARGET_X`: The x-coordinate of the center of a spatial view.
#' \item `SPATIAL_TARGET_Y`: The y-coordinate of the center of a spatial view.
#' \item `SPATIAL_TARGET_Z`: The z-coordinate of the center of a spatial view.
#' \item `HEATMAP_ZOOM_X`: The x-axis zoom level of a heatmap view.
#' \item `HEATMAP_ZOOM_Y`: The y-axis zoom level of a heatmap view.
#' \item `HEATMAP_TARGET_X`: The x-coordinate of the center of a heatmap view.
#' \item `HEATMAP_TARGET_Y`: The y-coordinate of the center of a heatmap view.
#' \item `CELL_FILTER`: A subset of cells to include after filtering.
#' \item `CELL_HIGHLIGHT`: A subset of cells to highlight.
#' \item `CELL_SET_SELECTION`: A subset of cell sets to select.
#' \item `CELL_SET_HIGHLIGHT`: A subset of cell sets to highlight.
#' \item `CELL_SET_COLOR`: A mapping from cell sets to colors.
#' \item `GENE_FILTER`: A subset of genes to include after filtering.
#' \item `GENE_HIGHLIGHT`: A subset of genes to highlight.
#' \item `GENE_SELECTION`: A subset of genes to select.
#' \item `GENE_EXPRESSION_COLORMAP`: The colormap to use for the gene expression scale.
#' \item `GENE_EXPRESSION_COLORMAP_RANGE`: The range of gene expression values to map.
#' \item `CELL_COLOR_ENCODING`: The color encoding to use for cell entities.
#' \item `SPATIAL_LAYERS`: Layer definitions for the spatial view.
#' \item `GENOMIC_ZOOM`: The zoom level of a higlass view.
#' \item `GENOMIC_TARGET_X`: The x-coordinate of the center of a higlass view.
#' \item `GENOMIC_TARGET_Y`: The y-coordinate of the center of a higlass view.
#' \item `ADDITIONAL_CELL_SETS`: User-defined cell sets.
#' }
#'
#' @export
#' @examples
#' 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$SCATTERPLOT, mapping = "umap")
#' qry_plot <- vc$add_view(qry_dataset, Component$SCATTERPLOT, mapping = "proj.umap")
#' vc$link_views(
#' c(ref_plot, qry_plot),
#' c(CoordinationType$EMBEDDING_TARGET_X, CoordinationType$EMBEDDING_TARGET_Y),
#' c_values = c(0, 0)
#' )
CoordinationType <- list(
META_COORDINATION_SCOPES = "metaCoordinationScopes",
META_COORDINATION_SCOPES_BY = "metaCoordinationScopesBy",
DATASET = "dataset",
EMBEDDING_TYPE = "embeddingType",
EMBEDDING_ZOOM = "embeddingZoom",
EMBEDDING_ROTATION = "embeddingRotation",
EMBEDDING_TARGET_X = "embeddingTargetX",
EMBEDDING_TARGET_Y = "embeddingTargetY",
EMBEDDING_TARGET_Z = "embeddingTargetZ",
SPATIAL_ZOOM = "spatialZoom",
SPATIAL_ROTATION = "spatialRotation",
SPATIAL_TARGET_X = "spatialTargetX",
SPATIAL_TARGET_Y = "spatialTargetY",
SPATIAL_TARGET_Z = "spatialTargetZ",
HEATMAP_ZOOM_X = "heatmapZoomX",
HEATMAP_ZOOM_Y = "heatmapZoomY",
HEATMAP_TARGET_X = "heatmapTargetX",
HEATMAP_TARGET_Y = "heatmapTargetY",
CELL_FILTER = "cellFilter",
CELL_HIGHLIGHT = "cellHighlight",
CELL_SET_SELECTION = "cellSetSelection",
CELL_SET_HIGHLIGHT = "cellSetHighlight",
CELL_SET_COLOR = "cellSetColor",
GENE_FILTER = "geneFilter",
GENE_HIGHLIGHT = "geneHighlight",
GENE_SELECTION = "geneSelection",
GENE_EXPRESSION_COLORMAP = "geneExpressionColormap",
GENE_EXPRESSION_COLORMAP_RANGE = "geneExpressionColormapRange",
FEATURE_VALUE_COLORMAP_RANGE = "featureValueColormapRange",
CELL_COLOR_ENCODING = "cellColorEncoding",
SPATIAL_LAYERS = "spatialLayers",
GENOMIC_ZOOM = "genomicZoom",
GENOMIC_TARGET_X = "genomicTargetX",
GENOMIC_TARGET_Y = "genomicTargetY",
ADDITIONAL_CELL_SETS = "additionalCellSets"
)
#' Enumeration of Data Type values
#'
#' The \code{DataType} list contains an enumeration of
#' valid string constant values representing data types
#' for dataset files.
#' \itemize{
#' \item `CELLS`: The `cells` data type.
#' \item `CELL_SETS`: The `cell-sets` data type.
#' \item `EXPRESSION_MATRIX`: The `expression-matrix` data type.
#' \item `MOLECULES`: The `molecules` data type.
#' \item `NEIGHBORHOODS`: The `neighborhoods` data type.
#' \item `RASTER`: The `raster` data type.
#' }
#'
#' @export
#' @examples
#' base_url <- "http://localhost:8000/"
#' 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$CELLS_JSON
#' )
DataType <- list(
CELLS = "cells",
CELL_SETS = "cell-sets",
EXPRESSION_MATRIX = "expression-matrix",
MOLECULES = "molecules",
NEIGHBORHOODS = "neighborhoods",
RASTER = "raster"
)
#' Enumeration of File Type values
#'
#' The \code{FileType} list contains an enumeration of
#' valid string constant values representing file types
#' for dataset files.
#' \itemize{
#' \item `CELLS_JSON`: The `cells.json` file type.
#' \item `MOLECULES_JSON`: The `molecules.json` file type.
#' \item `NEIGHBORHOODS_JSON`: The `neighborhoods.json` file type.
#' \item `RASTER_JSON`: The `raster.json` file type.
#' \item `CELL_SETS_JSON`: The `cell-sets.json` file type.
#' \item `CLUSTERS_JSON`: The `clusters.json` file type.
#' \item `EXPRESSION_MATRIX_ZARR`: The `expression-matrix.zarr` file type.
#' }
#'
#' @export
#' @examples
#' base_url <- "http://localhost:8000/"
#' vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
#' dataset <- vc$add_dataset("My dataset")$add_file(
#' url = paste0(base_url, "cells.json"),
#' file_type = FileType$CELLS_JSON
#' )
FileType <- list(
CELLS_JSON = "cells.json",
MOLECULES_JSON = "molecules.json",
NEIGHBORHOODS_JSON = "neighborhoods.json",
RASTER_JSON = "raster.json",
RASTER_OME_ZARR = "raster.ome-zarr",
CELL_SETS_JSON = "cell-sets.json",
CLUSTERS_JSON = "clusters.json",
EXPRESSION_MATRIX_ZARR = "expression-matrix.zarr",
ANNDATA_ZARR = "anndata.zarr",
ANNDATA_CELLS_ZARR = "anndata-cells.zarr",
ANNDATA_CELL_SETS_ZARR = "anndata-cell-sets.zarr",
ANNDATA_EXPRESSION_MATRIX_ZARR = "anndata-expression-matrix.zarr"
)
#' Enumeration of Component values
#'
#' The \code{Component} list contains an enumeration of
#' valid string constant values representing components.
#' \itemize{
#' \item `SCATTERPLOT`: The `scatterplot` component.
#' \item `SPATIAL`: The `spatial` component.
#' \item `DESCRIPTION`: The `description` component.
#' \item `STATUS`: The `status` component.
#' \item `CELL_SETS`: The `cellSets` component.
#' \item `HEATMAP`: The `heatmap` component.
#' \item `LAYER_CONTROLLER`: The `layerController` component.
#' \item `CELL_SET_SIZES`: The `cellSetSizes` component.
#' \item `GENES`: The `genes` component.
#' }
#'
#'
#' @export
#' @examples
#' vc <- VitessceConfig$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)
#' vc$widget()
Component <- list(
SCATTERPLOT = "scatterplot",
SPATIAL = "spatial",
DESCRIPTION = "description",
STATUS = "status",
CELL_SETS = "cellSets",
OBS_SETS = "obsSets",
HEATMAP = "heatmap",
LAYER_CONTROLLER = "layerController",
HIGLASS = "higlass",
CELL_SET_SIZES = "cellSetSizes",
GENES = "genes",
FEATURE_LIST = "featureList"
)
vitessce/vitessce-r documentation built on Oct. 12, 2024, 11:47 p.m.
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#' Enumeration of Coordination Type values
#'
#' The \code{CoordinationType} list contains an enumeration of
#' valid string constant values representing coordination types
#' in the coordination space.
#' \itemize{
#' \item `DATASET`: The dataset to be used for a view.
#' \item `EMBEDDING_TYPE`: The type of embedding to be used in the embedding scatterplot view, for example "UMAP" or "t-SNE".
#' \item `EMBEDDING_ZOOM`: The zoom level of an embedding scatterplot view.
#' \item `EMBEDDING_ROTATION`: The rotation of an embedding scatterplot view.
#' \item `EMBEDDING_TARGET_X`: The x-axis center of an embedding scatterplot view.
#' \item `EMBEDDING_TARGET_Y`: The y-axis center of an embedding scatterplot view.
#' \item `EMBEDDING_TARGET_Z`: The z-axis center of an embedding scatterplot view.
#' \item `SPATIAL_ZOOM`: The zoom level of a spatial view.
#' \item `SPATIAL_ROTATION`: The rotation of a spatial view.
#' \item `SPATIAL_TARGET_X`: The x-coordinate of the center of a spatial view.
#' \item `SPATIAL_TARGET_Y`: The y-coordinate of the center of a spatial view.
#' \item `SPATIAL_TARGET_Z`: The z-coordinate of the center of a spatial view.
#' \item `HEATMAP_ZOOM_X`: The x-axis zoom level of a heatmap view.
#' \item `HEATMAP_ZOOM_Y`: The y-axis zoom level of a heatmap view.
#' \item `HEATMAP_TARGET_X`: The x-coordinate of the center of a heatmap view.
#' \item `HEATMAP_TARGET_Y`: The y-coordinate of the center of a heatmap view.
#' \item `CELL_FILTER`: A subset of cells to include after filtering.
#' \item `CELL_HIGHLIGHT`: A subset of cells to highlight.
#' \item `CELL_SET_SELECTION`: A subset of cell sets to select.
#' \item `CELL_SET_HIGHLIGHT`: A subset of cell sets to highlight.
#' \item `CELL_SET_COLOR`: A mapping from cell sets to colors.
#' \item `GENE_FILTER`: A subset of genes to include after filtering.
#' \item `GENE_HIGHLIGHT`: A subset of genes to highlight.
#' \item `GENE_SELECTION`: A subset of genes to select.
#' \item `GENE_EXPRESSION_COLORMAP`: The colormap to use for the gene expression scale.
#' \item `GENE_EXPRESSION_COLORMAP_RANGE`: The range of gene expression values to map.
#' \item `CELL_COLOR_ENCODING`: The color encoding to use for cell entities.
#' \item `SPATIAL_LAYERS`: Layer definitions for the spatial view.
#' \item `GENOMIC_ZOOM`: The zoom level of a higlass view.
#' \item `GENOMIC_TARGET_X`: The x-coordinate of the center of a higlass view.
#' \item `GENOMIC_TARGET_Y`: The y-coordinate of the center of a higlass view.
#' \item `ADDITIONAL_CELL_SETS`: User-defined cell sets.
#' }
#'
#' @export
#' @examples
#' 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")
#' qry_plot <- vc$add_view(qry_dataset, Component$SCATTERPLOT, mapping = "proj.umap")
#' vc$link_views(
#' c(ref_plot, qry_plot),
#' c(CoordinationType$EMBEDDING_TARGET_X, CoordinationType$EMBEDDING_TARGET_Y),
#' c_values = c(0, 0)
#' )
CoordinationType <- list(
META_COORDINATION_SCOPES = "metaCoordinationScopes",
META_COORDINATION_SCOPES_BY = "metaCoordinationScopesBy",
DATASET = "dataset",
EMBEDDING_TYPE = "embeddingType",
EMBEDDING_ZOOM = "embeddingZoom",
EMBEDDING_ROTATION = "embeddingRotation",
EMBEDDING_TARGET_X = "embeddingTargetX",
EMBEDDING_TARGET_Y = "embeddingTargetY",
EMBEDDING_TARGET_Z = "embeddingTargetZ",
SPATIAL_ZOOM = "spatialZoom",
SPATIAL_ROTATION = "spatialRotation",
SPATIAL_TARGET_X = "spatialTargetX",
SPATIAL_TARGET_Y = "spatialTargetY",
SPATIAL_TARGET_Z = "spatialTargetZ",
HEATMAP_ZOOM_X = "heatmapZoomX",
HEATMAP_ZOOM_Y = "heatmapZoomY",
HEATMAP_TARGET_X = "heatmapTargetX",
HEATMAP_TARGET_Y = "heatmapTargetY",
CELL_FILTER = "cellFilter",
CELL_HIGHLIGHT = "cellHighlight",
CELL_SET_SELECTION = "cellSetSelection",
CELL_SET_HIGHLIGHT = "cellSetHighlight",
CELL_SET_COLOR = "cellSetColor",
GENE_FILTER = "geneFilter",
GENE_HIGHLIGHT = "geneHighlight",
GENE_SELECTION = "geneSelection",
GENE_EXPRESSION_COLORMAP = "geneExpressionColormap",
GENE_EXPRESSION_COLORMAP_RANGE = "geneExpressionColormapRange",
FEATURE_VALUE_COLORMAP_RANGE = "featureValueColormapRange",
CELL_COLOR_ENCODING = "cellColorEncoding",
SPATIAL_LAYERS = "spatialLayers",
GENOMIC_ZOOM = "genomicZoom",
GENOMIC_TARGET_X = "genomicTargetX",
GENOMIC_TARGET_Y = "genomicTargetY",
ADDITIONAL_CELL_SETS = "additionalCellSets"
)
#' Enumeration of Data Type values
#'
#' The \code{DataType} list contains an enumeration of
#' valid string constant values representing data types
#' for dataset files.
#' \itemize{
#' \item `CELLS`: The `cells` data type.
#' \item `CELL_SETS`: The `cell-sets` data type.
#' \item `EXPRESSION_MATRIX`: The `expression-matrix` data type.
#' \item `MOLECULES`: The `molecules` data type.
#' \item `NEIGHBORHOODS`: The `neighborhoods` data type.
#' \item `RASTER`: The `raster` data type.
#' }
#'
#' @export
#' @examples
#' base_url <- "http://localhost:8000/"
#' 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
#' )
DataType <- list(
CELLS = "cells",
CELL_SETS = "cell-sets",
EXPRESSION_MATRIX = "expression-matrix",
MOLECULES = "molecules",
NEIGHBORHOODS = "neighborhoods",
RASTER = "raster"
)
#' Enumeration of File Type values
#'
#' The \code{FileType} list contains an enumeration of
#' valid string constant values representing file types
#' for dataset files.
#' \itemize{
#' \item `CELLS_JSON`: The `cells.json` file type.
#' \item `MOLECULES_JSON`: The `molecules.json` file type.
#' \item `NEIGHBORHOODS_JSON`: The `neighborhoods.json` file type.
#' \item `RASTER_JSON`: The `raster.json` file type.
#' \item `CELL_SETS_JSON`: The `cell-sets.json` file type.
#' \item `CLUSTERS_JSON`: The `clusters.json` file type.
#' \item `EXPRESSION_MATRIX_ZARR`: The `expression-matrix.zarr` file type.
#' }
#'
#' @export
#' @examples
#' base_url <- "http://localhost:8000/"
#' vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
#' dataset <- vc$add_dataset("My dataset")$add_file(
#' url = paste0(base_url, "cells.json"),
#' file_type = FileType$CELLS_JSON
#' )
FileType <- list(
CELLS_JSON = "cells.json",
MOLECULES_JSON = "molecules.json",
NEIGHBORHOODS_JSON = "neighborhoods.json",
RASTER_JSON = "raster.json",
RASTER_OME_ZARR = "raster.ome-zarr",
CELL_SETS_JSON = "cell-sets.json",
CLUSTERS_JSON = "clusters.json",
EXPRESSION_MATRIX_ZARR = "expression-matrix.zarr",
ANNDATA_ZARR = "anndata.zarr",
ANNDATA_CELLS_ZARR = "anndata-cells.zarr",
ANNDATA_CELL_SETS_ZARR = "anndata-cell-sets.zarr",
ANNDATA_EXPRESSION_MATRIX_ZARR = "anndata-expression-matrix.zarr"
)
#' Enumeration of Component values
#'
#' The \code{Component} list contains an enumeration of
#' valid string constant values representing components.
#' \itemize{
#' \item `SCATTERPLOT`: The `scatterplot` component.
#' \item `SPATIAL`: The `spatial` component.
#' \item `DESCRIPTION`: The `description` component.
#' \item `STATUS`: The `status` component.
#' \item `CELL_SETS`: The `cellSets` component.
#' \item `HEATMAP`: The `heatmap` component.
#' \item `LAYER_CONTROLLER`: The `layerController` component.
#' \item `CELL_SET_SIZES`: The `cellSetSizes` component.
#' \item `GENES`: The `genes` component.
#' }
#'
#'
#' @export
#' @examples
#' 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$layout(description)
#' vc$widget()
Component <- list(
SCATTERPLOT = "scatterplot",
SPATIAL = "spatial",
DESCRIPTION = "description",
STATUS = "status",
CELL_SETS = "cellSets",
OBS_SETS = "obsSets",
HEATMAP = "heatmap",
LAYER_CONTROLLER = "layerController",
HIGLASS = "higlass",
CELL_SET_SIZES = "cellSetSizes",
GENES = "genes",
FEATURE_LIST = "featureList"
)
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