stroke visual channel

Usage

visual_channel_stroke(
  field = NULL,
  title = NULL,
  type = NULL,
  scaleOffset = NULL,
  legend = NULL,
  grid = NULL,
  axis = NULL,
  aggregate = NULL,
  ...
)

Arguments

field: A character. Name of the data field.
title: A character. Title of the legend. Default: undefined.
type: A character. Must be "genomic". Specify the data type.
scaleOffset: A number vector of the form c(1, 2). Whether to use offset of the domain proportionally. This is bound to brushes on the color legend. Default: c(0, 1).
legend: A Boolean. Whether to display legend. Default: FALSE.
grid: A Boolean. Whether to display grid. Default: FALSE.
axis: A character. One of "none", "top", "bottom", "left", "right". Specify where should the axis be put.
aggregate: A character. One of "max", "min", "mean", "bin", "count". Specify how to aggregate data. Default: undefined.
...: Any other parameters to pass to gosling.js.

Value

List object.

Details

For more info visit http://gosling-lang.org/docs/visual-channel#stroke

Examples

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

  track5_styles <- default_track_styles(
    legendTitle = "SV Class"
  )
  track5_data <- track_data(
    url = "https://s3.amazonaws.com/gosling-lang.org/data/cancer/rearrangement.PD35930a.csv",
    type = "csv",
    genomicFieldsToConvert = json_list(
      json_list(
        chromosomeField = "chr1",
        genomicFields = c("start1", "end1")
      ),
      json_list(
        chromosomeField = "chr2",
        genomicFields = c("start2", "end2")
      )
    )
  )
  track5_tracks <- add_multi_tracks(
    add_single_track(
      mark = "rect"
    ),
    add_single_track(
      mark = "withinLink", x = visual_channel_x(linkingId = "mid-scale"),
      strokeWidth = 0
    )
  )
  track5_color <- visual_channel_color(
    field = "svclass",
    type = "nominal",
    legend = TRUE,
    domain = json_list(
      "tandem-duplication", "translocation", "deletion", "inversion"
    ),
    range = json_list(
      "#569C4D", "#4C75A2", "#DA5456", "#EA8A2A"
    )
  )
  track5_stroke <- visual_channel_stroke(
    field = "svclass",
    type = "nominal",
    domain = json_list(
      "tandem-duplication", "translocation", "deletion", "inversion"
    ),
    range = json_list(
      "#569C4D", "#4C75A2", "#DA5456", "#EA8A2A"
    )
  )
  track5_x <- visual_channel_x(field = "start1", type = "genomic")
  track5_xe <- visual_channel_x(field = "end2", type = "genomic")
  track5 <- add_single_track(
    id = "track5", title = "Structural Variant",
    data = track5_data, mark = "withinLink",
    x = track5_x, xe = track5_xe,
    color = track5_color, width = 500, height = 80, stroke = track5_stroke,
    strokeWidth = 1, opacity = 0.6, style = track5_styles
  )

  composed_track <- compose_view(
    multi = TRUE,
    tracks = add_multi_tracks(
      track5
    ),
    xOffset = 190, layout = "circular", spacing = 1
  )

  composed_views <- arrange_views(
    views = composed_track,
    arrangement = "vertical"
  )

  ui <- fluidPage(
    use_gosling(),
    fluidRow(
      column(6, goslingOutput("gosling_plot"))
    )
  )


  server <- function(input, output, session) {
    output$gosling_plot <- renderGosling({
      gosling(
        component_id = "component_2",
        composed_views, clean_braces = FALSE
      )
    })
  }

  shinyApp(ui, server)

}