In vitessce/vitessceR: Create Interactive Single-cell Visualizations with the 'Vitessce' JavaScript Library

knitr::opts_knit$set(
  root.dir = dirname(dirname(getwd())),
  rmarkdown.pandoc.to = knitr::opts_knit$get("rmarkdown.pandoc.to")
)

The following is an example of usage of the widget to visualize a remote OME-TIFF image file.

First, configure the Vitessce widget:

library(vitessceR)

# Define the image file options object.
file_options = obj_list(
  schemaVersion = "0.0.2",
  images = list(
      obj_list(
        name = "My Image",
        type = "ome-tiff",
        url = "https://vitessce-demo-data.storage.googleapis.com/exemplar-001/exemplar-001.pyramid.ome.tif"
      )
  ),
  renderLayers = list(
    "My Image"
  )
)

# Create Vitessce view config
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
dataset <- vc$add_dataset("My dataset")$add_file(
  data_type = DataType$RASTER,
  file_type = FileType$RASTER_JSON,
  options = file_options
)
spatial <- vc$add_view(dataset, Component$SPATIAL)
spatial_layers <- vc$add_view(dataset, Component$LAYER_CONTROLLER)
status <- vc$add_view(dataset, Component$STATUS)
desc <- vc$add_view(dataset, Component$DESCRIPTION)
desc <- desc$set_props(description = "Visualization of an OME-TIFF file.")
vc$layout(hconcat(
  spatial,
  hconcat(spatial_layers, vconcat(desc, status))
))

# Render the Vitessce widget
vc$widget(theme = "light", width = "100%")

if(!is.null(knitr::opts_knit$get("rmarkdown.pandoc.to")) && knitr::opts_knit$get("rmarkdown.pandoc.to") == "html") {
  vc$widget(theme = "light", width = "100%")
}

vitessce/vitessceR documentation built on Oct. 12, 2024, 12:24 a.m.