VitessceConfig: VitessceConfig Class
In vitessce/vitessceR: Create Interactive Single-cell Visualizations with the 'Vitessce' JavaScript Library
VitessceConfig R Documentation
VitessceConfig Class
Description
Class representing a Vitessce view config.
Details
VitessceConfig
Public fields
configThe internal representation of the view config.
base_dirThe base directory for the config.
Methods
Public methods
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Method new()
Create a new config object.
Usage
VitessceConfig$new(schema_version, name = NA, description = NA, base_dir = NA)
Arguments
schema_versionThe Vitessce config schema version to use.
nameA name for the config.
descriptionA description for the config.
Returns
A new VitessceConfig object.
Method add_dataset()
Add a dataset to the config.
Usage
VitessceConfig$add_dataset(name, uid = NA)
Arguments
nameA name for the dataset.
uidA unique ID for the dataset. Optional. Created automatically if not provided.
Returns
A new VitessceConfigDataset object.
Examples
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
Method add_view()
Add a view to the config.
Usage
VitessceConfig$add_view(
dataset,
component,
x = NA,
y = NA,
w = NA,
h = NA,
mapping = NA
)
Arguments
datasetThe dataset object to associate with this view.
componentThe name of a component to render in this view.
xThe x-coordinate of the view in the layout.
yThe y-coordinate of the view in the layout.
wThe width of the view in the layout.
hThe height of the view in the layout.
mappingAn optional convenience parameter for setting the CoordinationType$EMBEDDING_TYPE coordination value if the component isComponent$SCATTERPLOT.
Returns
A new VitessceConfigView object.
Examples
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
spatial <- vc$add_view(ds, "spatial")
Method add_coordination()
Add a coordination scope to the config, for one or more coordination types.
Usage
VitessceConfig$add_coordination(c_types)
Arguments
c_typesThe coordination types for which to create new coordination scopes.
Returns
A list of new VitessceConfigCoordinationScope objects.
Examples
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
spatial <- vc$add_view(ds, "spatial")
c_scopes <- vc$add_coordination(c("spatialZoom", "spatialTargetX"))
spatial$use_coordination(c_scopes)
Method add_meta_coordination()
Usage
VitessceConfig$add_meta_coordination()
Method add_coordination_by_dict()
Usage
VitessceConfig$add_coordination_by_dict(input_val)
Method link_views_by_dict()
Usage
VitessceConfig$link_views_by_dict(views, input_val, meta = TRUE)
Method layout()
Define the layout of views.
Usage
VitessceConfig$layout(view_concat)
Arguments
view_concatA concatenation of views.
Returns
Self, to allow chaining.
Examples
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")
Method link_views()
A convenience function for setting up new coordination scopes across a set of views.
Usage
VitessceConfig$link_views(views, c_types, c_values = NA, raw = FALSE)
Arguments
viewsAn array of view objects to link together.
c_typesThe coordination types on which to coordinate the views.
c_valuesInitial values corresponding to each coordination type.
Should have the same length as the c_types array. Optional.
rawShould the coordination values be set using
VitessceConfigCoordinationScope$set_value() or
VitessceConfigCoordinationScope$set_value_raw()? Use
when setting lists or similar more complex values.
Returns
Self, to allow chaining.
Examples
vc <- VitessceConfig$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$EMBEDDING_TARGET_Y),
c_values = c(0, 0)
)
Method to_list()
Convert the config to an R list. Helpful when converting the config to JSON.
Usage
VitessceConfig$to_list(base_url = NA)
Arguments
base_urlAn base URL to prepend to file paths.
Returns
A list that can be serialized to JSON.
Examples
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
vc_list <- vc$to_list(base_url = "http://localhost:8000")
Method get_routes()
Get a list of web server route objects corresponding to any local files which will need to be served.
Usage
VitessceConfig$get_routes()
Returns
A list of VitessceConfigServerStaticRoute.
Method widget()
Create an htmlwidget based on this config.
Usage
VitessceConfig$widget(...)
Arguments
...Passes extra keyword arguments to the vitessce_widget function.
themeThe theme of the widget, either "dark" or "light". Optional. By default, "dark".
widthThe width of the widget as a number or CSS string. Optional.
heightThe height of the widget as a number or CSS string. Optional.
portThe port for the local web server (which serves local dataset objects to the widget).
Optional. By default, uses open port between 8000 and 9000.
base_urlThe base URL for the web server. Optional.
By default, creates a localhost URL which includes the port.
serveShould local data be served by running a local web server with R plumber? By default, TRUE.
element_idAn element ID. Optional.
Returns
The Vitessce htmlwidget.
Examples
vc <- VitessceConfig$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$widget()
Method export()
Export the data associated with this configuration to a specified destination.
Usage
VitessceConfig$export(to = "files", with_config = FALSE, base_url = NA, ...)
Arguments
toWhere should the files be exported to? Values currently supported: "files"
with_configShould the Vitessce configuration be saved in the output directory as a JSON file?
base_urlIf with_config is TRUE, what base_url value should be used for creation of the JSON config?
...Extra parameters to pass through to the export function.
Returns
The Vitessce configuration as a list, with the base_url filled in.
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$layout(description)
vc$export(with_config = TRUE, base_url = "http://localhost:3000", out_dir = "./data")
Method clone()
The objects of this class are cloneable with this method.
Usage
VitessceConfig$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
## ------------------------------------------------
## Method `VitessceConfig$add_dataset`
## ------------------------------------------------
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
## ------------------------------------------------
## Method `VitessceConfig$add_view`
## ------------------------------------------------
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
spatial <- vc$add_view(ds, "spatial")
## ------------------------------------------------
## Method `VitessceConfig$add_coordination`
## ------------------------------------------------
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
spatial <- vc$add_view(ds, "spatial")
c_scopes <- vc$add_coordination(c("spatialZoom", "spatialTargetX"))
spatial$use_coordination(c_scopes)
## ------------------------------------------------
## Method `VitessceConfig$layout`
## ------------------------------------------------
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
spatial <- vc$add_view(ds, "spatial")
scatterplot <- vc$add_view(ds, "scatterplot")
## ------------------------------------------------
## Method `VitessceConfig$link_views`
## ------------------------------------------------
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)
)
## ------------------------------------------------
## Method `VitessceConfig$to_list`
## ------------------------------------------------
vc <- VitessceConfig$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")
## ------------------------------------------------
## Method `VitessceConfig$widget`
## ------------------------------------------------
vc <- VitessceConfig$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$widget()
## ------------------------------------------------
## Method `VitessceConfig$export`
## ------------------------------------------------
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$layout(description)
vc$export(with_config = TRUE, base_url = "http://localhost:3000", out_dir = "./data")
vitessce/vitessceR documentation built on Oct. 12, 2024, 12:24 a.m.
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| VitessceConfig | R Documentation |
VitessceConfig Class
Description
Class representing a Vitessce view config.
Details
VitessceConfig
Public fields
configThe internal representation of the view config.
base_dirThe base directory for the config.
Methods
Public methods
Method new()
Create a new config object.
Usage
VitessceConfig$new(schema_version, name = NA, description = NA, base_dir = NA)
Arguments
schema_versionThe Vitessce config schema version to use.
nameA name for the config.
descriptionA description for the config.
Returns
A new VitessceConfig object.
Method add_dataset()
Add a dataset to the config.
Usage
VitessceConfig$add_dataset(name, uid = NA)
Arguments
nameA name for the dataset.
uidA unique ID for the dataset. Optional. Created automatically if not provided.
Returns
A new VitessceConfigDataset object.
Examples
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
Method add_view()
Add a view to the config.
Usage
VitessceConfig$add_view( dataset, component, x = NA, y = NA, w = NA, h = NA, mapping = NA )
Arguments
datasetThe dataset object to associate with this view.
componentThe name of a component to render in this view.
xThe x-coordinate of the view in the layout.
yThe y-coordinate of the view in the layout.
wThe width of the view in the layout.
hThe height of the view in the layout.
mappingAn optional convenience parameter for setting the
CoordinationType$EMBEDDING_TYPEcoordination value if the component isComponent$SCATTERPLOT.
Returns
A new VitessceConfigView object.
Examples
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
spatial <- vc$add_view(ds, "spatial")
Method add_coordination()
Add a coordination scope to the config, for one or more coordination types.
Usage
VitessceConfig$add_coordination(c_types)
Arguments
c_typesThe coordination types for which to create new coordination scopes.
Returns
A list of new VitessceConfigCoordinationScope objects.
Examples
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
spatial <- vc$add_view(ds, "spatial")
c_scopes <- vc$add_coordination(c("spatialZoom", "spatialTargetX"))
spatial$use_coordination(c_scopes)
Method add_meta_coordination()
Usage
VitessceConfig$add_meta_coordination()
Method add_coordination_by_dict()
Usage
VitessceConfig$add_coordination_by_dict(input_val)
Method link_views_by_dict()
Usage
VitessceConfig$link_views_by_dict(views, input_val, meta = TRUE)
Method layout()
Define the layout of views.
Usage
VitessceConfig$layout(view_concat)
Arguments
view_concatA concatenation of views.
Returns
Self, to allow chaining.
Examples
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")
Method link_views()
A convenience function for setting up new coordination scopes across a set of views.
Usage
VitessceConfig$link_views(views, c_types, c_values = NA, raw = FALSE)
Arguments
viewsAn array of view objects to link together.
c_typesThe coordination types on which to coordinate the views.
c_valuesInitial values corresponding to each coordination type. Should have the same length as the c_types array. Optional.
rawShould the coordination values be set using VitessceConfigCoordinationScope$set_value() or VitessceConfigCoordinationScope$set_value_raw()? Use when setting lists or similar more complex values.
Returns
Self, to allow chaining.
Examples
vc <- VitessceConfig$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$EMBEDDING_TARGET_Y),
c_values = c(0, 0)
)
Method to_list()
Convert the config to an R list. Helpful when converting the config to JSON.
Usage
VitessceConfig$to_list(base_url = NA)
Arguments
base_urlAn base URL to prepend to file paths.
Returns
A list that can be serialized to JSON.
Examples
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
vc_list <- vc$to_list(base_url = "http://localhost:8000")
Method get_routes()
Get a list of web server route objects corresponding to any local files which will need to be served.
Usage
VitessceConfig$get_routes()
Returns
A list of VitessceConfigServerStaticRoute.
Method widget()
Create an htmlwidget based on this config.
Usage
VitessceConfig$widget(...)
Arguments
...Passes extra keyword arguments to the
vitessce_widgetfunction.themeThe theme of the widget, either "dark" or "light". Optional. By default, "dark".
widthThe width of the widget as a number or CSS string. Optional.
heightThe height of the widget as a number or CSS string. Optional.
portThe port for the local web server (which serves local dataset objects to the widget). Optional. By default, uses open port between 8000 and 9000.
base_urlThe base URL for the web server. Optional. By default, creates a localhost URL which includes the port.
serveShould local data be served by running a local web server with R plumber? By default, TRUE.
element_idAn element ID. Optional.
Returns
The Vitessce htmlwidget.
Examples
vc <- VitessceConfig$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$widget()
Method export()
Export the data associated with this configuration to a specified destination.
Usage
VitessceConfig$export(to = "files", with_config = FALSE, base_url = NA, ...)
Arguments
toWhere should the files be exported to? Values currently supported: "files"
with_configShould the Vitessce configuration be saved in the output directory as a JSON file?
base_urlIf
with_configis TRUE, whatbase_urlvalue should be used for creation of the JSON config?...Extra parameters to pass through to the export function.
Returns
The Vitessce configuration as a list, with the base_url filled in.
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$layout(description)
vc$export(with_config = TRUE, base_url = "http://localhost:3000", out_dir = "./data")
Method clone()
The objects of this class are cloneable with this method.
Usage
VitessceConfig$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
## ------------------------------------------------
## Method `VitessceConfig$add_dataset`
## ------------------------------------------------
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
## ------------------------------------------------
## Method `VitessceConfig$add_view`
## ------------------------------------------------
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
spatial <- vc$add_view(ds, "spatial")
## ------------------------------------------------
## Method `VitessceConfig$add_coordination`
## ------------------------------------------------
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
spatial <- vc$add_view(ds, "spatial")
c_scopes <- vc$add_coordination(c("spatialZoom", "spatialTargetX"))
spatial$use_coordination(c_scopes)
## ------------------------------------------------
## Method `VitessceConfig$layout`
## ------------------------------------------------
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
ds <- vc$add_dataset("My dataset")
spatial <- vc$add_view(ds, "spatial")
scatterplot <- vc$add_view(ds, "scatterplot")
## ------------------------------------------------
## Method `VitessceConfig$link_views`
## ------------------------------------------------
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)
)
## ------------------------------------------------
## Method `VitessceConfig$to_list`
## ------------------------------------------------
vc <- VitessceConfig$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")
## ------------------------------------------------
## Method `VitessceConfig$widget`
## ------------------------------------------------
vc <- VitessceConfig$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$widget()
## ------------------------------------------------
## Method `VitessceConfig$export`
## ------------------------------------------------
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$layout(description)
vc$export(with_config = TRUE, base_url = "http://localhost:3000", out_dir = "./data")
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