Data object builder

Build the data object for gosling plots

Usage

track_data(
  url = NULL,
  type,
  separator = NULL,
  sampleLength = NULL,
  headerNames = NULL,
  genomicFields = NULL,
  chromosomeField = NULL,
  genomicFieldsToConvert = NULL,
  ...
)

Arguments

url

A character. Specify the URL address of the data file.

type

A character. Type of data. One of "csv", "json", "bigwig", "bam", "vcf", "vector", "multivec" and "beddb". For usage refer to http://gosling-lang.org/docs/data#supported-data-formats.

separator

A character. Specify file separator, Default: ','

sampleLength

A number. Specify the number of rows loaded from the URL. Default: 1000

headerNames

A character vector. Specify the names of data fields if a CSV file does not have header row.

genomicFields

A character vector. Specify the name of genomic data fields.

chromosomeField

A character. Specify the name of chromosome data fields.

genomicFieldsToConvert

Define the genomic fields from the data in list format. Experimental Property. Each object follows the format "chromosomeField":"string","genomicFields":"string[]" ( )

...

Any other parameters passed to json data object.

Value

list of data specs

Details

For info visit http://gosling-lang.org/docs/data. Check the various supported data formats and their parameters. All of them can be constructed using this function.

Examples

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

  # View 2 Track 3----
  view2_track3_data <- track_data(
    url = "https://server.gosling-lang.org/api/v1/tileset_info/?d=NC_045512_2-multivec",
    type = "multivec",
    row = "base",
    column = "position",
    value = "count",
    categories = c("A", "T", "G", "C"),
    start = "start",
    end = "end"
  )

  view2_track3a <- add_single_track(
    mark = "bar",
    y = visual_channel_y(
      field = "count", type = "quantitative", axis = "none"
    )
  )

  view2_track3b <- add_single_track(
    dataTransform = track_data_transform(
      type = "filter",
      field = "count",
      oneOf = list(0),
      not = TRUE
    ),
    mark = "text",
    x = visual_channel_x(
      field = "start", type = "genomic"
    ),
    xe = visual_channel_x(
      field = "end", type = "genomic"
    ),
    size = 24,
    color = "white",
    visibility = list(
      list(
        operation = "less-than",
        measure = "width",
        threshold = "|xe-x|",
        transitionPadding = 30,
        target = "mark"
      ),
      list(
        operation = "LT",
        measure = "zoomLevel",
        threshold = 40,
        target = "track"
      )
    )
  )

  view2_track3_x <- visual_channel_x(
    field = "position", type = "genomic"
  )

  view2_track3_color <- visual_channel_color(
    field = "base",
    type = "nominal",
    domain = c("A", "T", "G", "C"),
    legend = TRUE
  )

  view2_track3_text <- visual_channel_text(
    field = "base", type = "nominal"
  )

  view2_track3_style <- default_track_styles(
    inlineLegend = TRUE
  )

  view2_track3 <- add_single_track(
    title = "NC_045512.2 Sequence",
    alignment = "overlay",
    data = view2_track3_data,
    tracks = add_multi_tracks(
      view2_track3a, view2_track3b
    ),
    x = view2_track3_x,
    color = view2_track3_color,
    text = view2_track3_text,
    style = view2_track3_style,
    width = 800, height = 40
  )

  view2 <- compose_view(
    multi = TRUE,
    centerRadius = 0,
    xDomain = list(interval = c(1, 29903)),
    linkingId = "detail",
    alignment = "stack",
    tracks = add_multi_tracks(
      view2_track3
    )
  )

  combined_view <- arrange_views(
    title = "SARS-CoV-2",
    subtitle = "Data Source: WashU Virus Genome Browser, NCBI, GISAID",
    assembly = list(list("NC_045512.2", 29903)),
    layout = "linear",
    spacing = 50,
    views = list(view2),
    listify = FALSE
  )

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


  server <- function(input, output, session) {
    output$gosling_plot <- renderGosling({
      gosling(
        component_id = "sars_cov2",
        combined_view
      )
    })
  }

  shinyApp(ui, server)
}