Add a single track

Add a single track to the plot of a mark type ( plot type ). This function constructs a single track from the inputs. The inputs can be id, data, mark etc. Please check gosling.js documentation for usage.

Usage

add_single_track(
  id = NULL,
  data = NULL,
  mark = NULL,
  assembly = NULL,
  row = NULL,
  size = NULL,
  color = NULL,
  strokeWidth = NULL,
  opacity = NULL,
  x = NULL,
  xe = NULL,
  x1 = NULL,
  x1e = NULL,
  y = NULL,
  stroke = NULL,
  width = NULL,
  height = NULL,
  dataTransform = NULL,
  ...
)

Arguments

id

Optional argument to assign an id to the track.

data

An object of from track_data() function.

mark

Type of plot. One of c("point", "line", "rect", "bar", "area", "link", "triangle", "text"). Each mark type has some supported visual channel.

Different marks support different visual channels:

• point: x, y, row, size, color, strokeWidth, opacity

• line: x, y, row, color, strokeWidth

• rect: x, xe, row, color, strokeWidth, opacity

• bar: x, y, row, color, strokeWidth, opacity

• area: x, y, row, color, strokeWidth

• link: x, xe, x1, x1e, color, opacity

• triangle: x, xe, row, size, color, opacity

• text: x, xe, row, color, opacity

For more info visit http://gosling-lang.org/tutorials/

assembly

Currently support "hg38", "hg19", "hg18", "hg17", "hg16", "mm10", "mm9". Defaults to "hg38".

row

An object of from visual_channel_row().

size

An object of from visual_channel_size() OR an atomic number.

color

An object of from visual_channel_color() OR and atomic character hex code of the form "#123456".

strokeWidth

An object of from visual_channel_stroke_width() OR an atomic number.

opacity

An object of from visual_channel_opacity() OR and atomic ratio from 0 to 1.

x

An object of from visual_channel_x() OR an atomic value.

xe

An object of from visual_channel_x() OR an atomic value.

x1

An object of from visual_channel_x() OR an atomic value.

x1e

An object of from visual_channel_x() OR an atomic value.

y

An object of from visual_channel_y() OR an atomic value.

stroke

An object of from visual_channel_stroke() function OR a character of hex color code like "#123456".

width

A number interpreted in units of pixel.

height

A number interpreted in units of pixel.

dataTransform

An object of from track_data_transform() function.

...

Any other arguments to be passed onto gosling.js.

Value

list object.

Examples

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

  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(
          "download_png",
          "PNG",
          icon = icon("cloud-arrow-down")
        )
      )
    )
  )


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

    observeEvent(input$download_png, {
      export_png(component_id = "component_1")
    })
  }

  shinyApp(ui, server)

}