Zoom to

Zooms to a specific genomic position with the animated transition.

Usage

zoom_to(
  component_id,
  view_id,
  position,
  padding = 0,
  duration = 1000,
  session = getDefaultReactiveDomain()
)

Arguments

component_id

A character. The id of the component_id prop passed to the GoslingComponent function.

view_id

A character. The ID of a view that you want to control. This ID is consistent to what you specify as track.id in your spec.

position

A character. The genomic position that your view should be navigated to. You can either specify chromosome (e.g., chr1) or a chromosome and range pair (e.g., chr1:1-10000).

padding

A numeric. This determines the padding around the specified position. The unit of this number is a base pair (Default: 0).

duration

A numeric. A duration of the animated transition in ms (Default: 1000).

session

A shiny session object.

Value

None.

Examples

if(interactive()) {
  library(shiny)
  library(shiny.gosling)

  chromosome_options <- c(
    "Chr 1" = "chr1",
    "Chr 2" = "chr2",
    "Chr X" = "chrX",
    "Chr Y" = "chrY"
  )

  cistrome_data <-
    "https://server.gosling-lang.org/api/v1/tileset_info/?d=cistrome-multivec"

  single_track <- add_single_track(
    id = "track1",
    data = track_data(
      url = cistrome_data,
      type = "multivec",
      row = "sample",
      column = "position",
      value = "peak",
      categories = c("sample 1", "sample 2", "sample 3", "sample 4"),
      binSize = 4,
    ),
    mark = "rect",
    x = visual_channel_x(field = "start", type = "genomic", axis = "top"),
    xe = visual_channel_x(field = "end", type = "genomic"),
    row = visual_channel_row(
      field = "sample",
      type = "nominal",
      legend = TRUE
    ),
    color = visual_channel_color(
      field = "peak",
      type = "quantitative",
      legend = TRUE
    ),
    tooltip = visual_channel_tooltips(
      visual_channel_tooltip(field = "start", type = "genomic",
                             alt = "Start Position"),
      visual_channel_tooltip(field = "end", type = "genomic",
                             alt = "End Position"),
      visual_channel_tooltip(
        field = "peak",
        type = "quantitative",
        alt = "Value",
        format = "0.2"
      )
    ),
    width = 600,
    height = 130
  )

  single_composed_track <- compose_view(
    tracks = single_track
  )

  single_composed_views <- arrange_views(
    title = "Single Track",
    subtitle = "This is the simplest single track visualization with a linear layout",
    layout = "circular", #"linear"
    views = single_composed_track,
    xDomain = list(
      chromosome = "chr1",
      interval = c(1, 3000500)
    )
  )

  ui <- fluidPage(
    use_gosling(),
    fluidRow(
      column(6, goslingOutput("gosling_plot")),
      column(
        1, br(), actionButton(
          "zoom_out",
          "Zoom To"
        )
      ),
      column(
        2,
        selectInput(
          "chromosomes",
          "Chromosome",
          selected = "chr1",
          choices = chromosome_options
        )
      )
    )
  )


  server <- function(input, output, session) {
    output$gosling_plot <- renderGosling({
      gosling(
        component_id = "component_1",
        single_composed_views,
        clean_braces = TRUE
      )
    })

    observeEvent(input$zoom_out, {
      zoom_to(
        component_id = "component_1",
        view_id = "track1",
        position = input$chromosomes
      )
    })
  }

  shinyApp(ui, server)

}