Package 'shiny.gosling'

Title: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization for R and Shiny
Description: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. http://gosling-lang.org/. This R package is based on gosling.js. It uses R functions to create gosling plots that could be embedded onto R Shiny apps.
Authors: Appsilon [aut, cre], Anirban Shaw [aut] , Federico Rivadeneira [aut] , Vedha Viyash [aut]
Maintainer: Appsilon <[email protected]>
License: LGPL-3
Version: 1.1.0
Built: 2024-07-15 02:31:10 UTC
Source: https://github.com/bioc/shiny.gosling

Help Index

Track data object builder for local csv files

Description

Get an object for using local csv to build plots

Usage

add_file_to_resource_path(file_path = NULL, object = NULL)

Arguments

file_path

A character. Specify the file_path to the local csv file.
object

A gr ranges object.

Value

list of data specs for a local csv file

Visual marks

Description

Visual marks (e.g., points, lines, and bars) are the basic graphical elements of a visualization.

Usage

add_mark(
  x = NULL,
  xe = NULL,
  x1 = NULL,
  x1e = NULL,
  y = NULL,
  strokeWidth = NULL,
  opacity = NULL,
  row = NULL,
  size = NULL,
  color = NULL,
  stroke = NULL
)

Arguments

x

An object returned by visual_channel_x().
xe

An object returned by visual_channel_x().
x1

An object returned by visual_channel_x().
x1e

An object returned by visual_channel_x().
y

An object returned by visual_channel_y().
strokeWidth

A number or an object returned by visual_channel_stroke_width().
opacity

A number or an object returned by visual_channel_opacity().
row

A factor data column Channel row is used with channel y to stratify a visualization with categorical values.
size

A number or an object returned by visual_channel_size().
color

A character or an object returned by visual_channel_color().
stroke

A number or an object returned by visual_channel_stroke().

Details

For info visit http://gosling-lang.org/docs/mark

Value

list of mark specifications

Combine single tracks.

Description

Combine single tracks.

Usage

add_multi_tracks(...)

Arguments

...

Multiple tracks from add_single_track() function.

Value

json list.

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)

}

Add a single track

Description

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)

}

Arrange views

Description

Arrange views from compose_view() function.

Usage

arrange_views(layout = NULL, views = NULL, listify = TRUE, ...)

Arguments

layout

One of "linear" or "circular".
views

An object from compose_view() function.
listify

A Boolean. Convert views to list..
...

More options passed to gosling.js.

Value

list object.

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)

}

atomic_values_to_list

Description

atomic_values_to_list

Usage

atomic_values_to_list(property_list)

Arguments

property_list

A character or number or another atomic value.

Value

List.

style of the brush mark

Description

Customize the style of the brush mark in the rangeSelect mouse event.

Usage

brush_styles(
  strokeWidth = NULL,
  strokeOpacity = NULL,
  stroke = NULL,
  opacity = NULL,
  color = NULL
)

Arguments

strokeWidth

A number. stroke width of the marks when mouse events are triggered.
strokeOpacity

A number.
stroke

A character. Stroke color of the marks when mouse events are triggered.
opacity

A number. Opacity of the marks when mouse events are triggered.
color

A character. Color of the marks when mouse events are triggered.

Details

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

Value

List object with brush styles.

Build gosling spec from R list

Description

Build gosling spec from R list

Usage

build_json(r_list, clean_braces = TRUE, pretty = TRUE, auto_unbox = TRUE)

Arguments

r_list

R list object built with other gosling functions
clean_braces

Whether to remove extra square brackets from the json string.
pretty

Whether to get json with indentation, line breaks etc.
auto_unbox

If TRUE will automatically unbox() all atomic vectors of length 1.

Value

json spec for the gosling output

Create react component

Description

Create react component

Usage

component(name)

Arguments

name

name of the react component

Value

function to create react element

Compose views

Description

Compose views from add_single_track() and add_multi_tracks() functions.

Usage

compose_view(
  multi = FALSE,
  layout = NULL,
  width = NULL,
  height = NULL,
  centerRadius = NULL,
  tracks,
  ...
)

Arguments

multi

Whether multiple tracks in the view.
layout

One of "linear" or "circular".
width

A number interpreted in units of pixel.
height

A number interpreted in units of pixel.
centerRadius

Specify the proportion of the radius of the center white space. A number between c(0,1), default=0.3
tracks

The tracks with add_multi_tracks() function.
...

More arguments passed along with view to gosling.js.

Value

list object.

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)

}

Default styles for tracks

Description

Default styles for tracks

Usage

default_track_styles(
  textStrokeWidth = NULL,
  textStroke = NULL,
  textFontWeight = NULL,
  textFontSize = NULL,
  textAnchor = NULL,
  select = NULL,
  outlineWidth = NULL,
  outline = NULL,
  mouseOver = NULL,
  matrixExtent = NULL,
  linkStyle = NULL,
  linkMinHeight = NULL,
  linkConnectionType = NULL,
  linePattern = NULL,
  legendTitle = NULL,
  inlineLegend = NULL,
  enableSmoothPath = NULL,
  dy = NULL,
  dx = NULL,
  dashed = NULL,
  curve = NULL,
  brush = NULL,
  backgroundOpacity = NULL,
  background = NULL,
  align = NULL,
  ...
)

Arguments

textStrokeWidth

A number. Specify the stroke width of text marks. Can also be specified using the strokeWidth channel option of text marks.
textStroke

A character. Specify the stroke of text marks. Can also be specified using the stroke channel option of text marks.
textFontWeight

A character. One of "bold", "normal". Specify the font weight of text marks.
textFontSize

A number. Specify the font size of text marks. Can also be specified using the size channel option of text marks.
textAnchor

A character. One of "start", "middle", "end". Specify the alignment of text marks to a given point.
select

An object returned by event_styles(). Customize visual effects of rangeSelect events on marks.
outlineWidth

A number.
outline

A character.
mouseOver

An object returned by event_styles(). Customize visual effects of mouseOver events on marks.
matrixExtent

A character.One of "full", "upper-right", "lower-left". Determine to show only one side of the diagonal in a HiGlass matrix. Default: "full".
linkStyle

A character. One of "elliptical", "circular", "straight", "experimentalEdgeBundling". The style of withinLink and betweenLink marks. Default: 'circular' 'elliptical' will be used as a default option.
linkMinHeight

A number. The minimum height of withinLink and betweenLink marks. Unit is a percentage Default: 0.5.
linkConnectionType

A character. One of "straight", "curve", "corner". Specify the connection type of betweenLink marks. Default: "corner".
linePattern

A list of the form list(size="number",type="string"). One of "triangleLeft", "triangleRight".) Specify the pattern of dashes and gaps for rule marks.
legendTitle

A character. If defined, show legend title on the top or left.
inlineLegend

A Boolean. Specify whether to show legend in a single horizontal line?
enableSmoothPath

A Boolean. Whether to enable smooth paths when drawing curves. Default: FALSE.
dy

A number. Offset the position of marks in y direction. This property is currently only supported for text marks.
dx

A number. Offset the position of marks in x direction. This property is currently only supported for text marks.
dashed

An vector of number like c(1, 2). Specify the pattern of dashes and gaps for rule marks.
curve

A character. One of "top", "bottom", "left", "right". Specify the curve of rule marks.
brush

An object returned by brush_styles(). Customize the style of the brush mark in the rangeSelect mouse event.
backgroundOpacity

A number.
background

A character.
align

A character. One of "left", "right". Specify the alignment of marks. This property is currently only supported for triangle marks.
...

Any other styles to be passed to gosling.js.

Details

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

Value

List object with default styles.

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)

}

Mouse event styles

Description

The styles defined here will be applied to the targets of mouse events, such as a point mark after user click mouse.

Usage

event_styles(
  strokeWidth = NULL,
  strokeOpacity = NULL,
  stroke = NULL,
  opacity = NULL,
  color = NULL,
  arrange = NULL
)

Arguments

strokeWidth

A number. stroke width of the marks when mouse events are triggered.
strokeOpacity

A number.
stroke

A character. Stroke color of the marks when mouse events are triggered.
opacity

A number. Opacity of the marks when mouse events are triggered.
color

A character. Color of the marks when mouse events are triggered.
arrange

A character. One of "behind", "front". Show event effects behind or in front of marks.

Details

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

Value

List object with event styles.

Export PDF

Description

Exports PDF

Usage

export_pdf(
  component_id,
  transparent_background = FALSE,
  session = getDefaultReactiveDomain()
)

Arguments

component_id

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

A Boolean. Determine if the background should be transparent or not (Default: false).
session

A shiny session object.

Value

None.

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_pdf",
          "PDF",
          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_pdf, {
      export_pdf(component_id = "component_1")
    })
  }

  shinyApp(ui, server)

}

Export PNG

Description

Exports PNG

Usage

export_png(
  component_id,
  transparent_background = FALSE,
  session = getDefaultReactiveDomain()
)

Arguments

component_id

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

A Boolean. Determine if the background should be transparent or not (Default: false).
session

A shiny session object.

Value

None.

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)

}

Track data object builder for local csv files

Description

Get an object for using local csv to build plots

Usage

get_file_track_data(
  file_name,
  chromosomeField = NULL,
  genomicFields = NULL,
  separator = ",",
  sampleLength = 1000,
  headerNames = NULL,
  ...
)

Arguments

file_name

A character. Specify the file_name.
chromosomeField

A character. Specify the name of chromosome data fields.
genomicFields

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

Any other parameters passed to json data object.

Value

list of data specs for a local csv file

Build gosling plot object

Description

Build gosling plot object

Usage

gosling(component_id, composed_views, clean_braces = TRUE)

Arguments

component_id

Assign a component id to use other api like zoom.
composed_views

The views composed with arrange_views.
clean_braces

Whether to remove extra square brackets from the json string.

Value

Gosling component for rendering on R shiny apps

Examples

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

  # Circular track 1 ----
  circular_track1_data <- track_data(
    url = "https://server.gosling-lang.org/api/v1/tileset_info/?d=cistrome-multivec",
    type = "multivec",
    row = "sample",
    column = "position",
    value = "peak",
    categories = c("sample 1", "sample 2", "sample 3", "sample 4"),
    binSize = 4
  )

  circular_track1_x <- visual_channel_x(field = "start", type = "genomic")
  circular_track1_xe <- visual_channel_x(field = "end", type = "genomic")

  circular_track1_y <- visual_channel_y(field = "peak", type = "quantitative")

  circular_track1_row <- visual_channel_row(
    field = "sample", type = "nominal"
  )

  circular_track1_color <- visual_channel_color(
    field = "sample", type = "nominal"
  )

  circular_track1_tracks <- add_multi_tracks(
    add_single_track(
      mark = "bar"
    ),
    add_single_track(
      mark = "brush",
      x = visual_channel_x(linkingId = "detail-1"),
      color = "blue"
    ),
    add_single_track(
      mark = "brush",
      x = visual_channel_x(linkingId = "detail-2"),
      color = "red"
    )
  )

  circular_track1_styles <- default_track_styles(
    outlineWidth = 0
  )

  circular_track1 <- add_single_track(
    id = "circular_track1", alignment = "overlay", data = circular_track1_data,
    x = circular_track1_x, xe = circular_track1_xe,
    y = circular_track1_y, row = circular_track1_row,
    color = circular_track1_color,
    stroke = "black", strokeWidth = 0.3,
    tracks = circular_track1_tracks,
    style = circular_track1_styles,
    width = 500, height = 100
  )

  # Compose Circular track ----
  circular_composed_view <- compose_view(
    multi = TRUE,
    tracks = add_multi_tracks(
      circular_track1
    ),
    static = TRUE, layout = "circular", alignment = "stack"
  )

  # Arrange final view
  circular_linear_view <- arrange_views(
    arrangement = "horizontal",
    views = list(circular_composed_view)
  )




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


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

  shinyApp(ui, server)
}

Create Gosling component

Description

Create Gosling component

Usage

GoslingComponent(...)

Arguments

...

Name of component.

Value

A function to create the gosling component.

Setup gosling dependencies

Description

Setup gosling dependencies

Usage

goslingDependency()

Value

list of dependencies for Gosling

gosling output function

Description

gosling output function for shiny use. Must use this function instead of shiny output functions.

Usage

goslingOutput(outputId)

Arguments

outputId

ID of the output element

Value

reactOutput HTML for UI render

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)

}

is_atomic_field

Description

is_atomic_field

Usage

is_atomic_field(field_name)

Arguments

field_name

A character or number or another atomic value.

Value

List.

Create list

Description

Create list

Usage

json_list(...)

Arguments

...

Items to be put in a list

Value

list of items

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)
}

Remove null from list

Description

Remove null from list

Usage

list_rm_null(r_list)

Arguments

r_list

An r list with NULL values

Value

r list without NULL values

Print method for the gosling component

Description

Print method for the gosling component

Usage

## S3 method for class 'gosling'
print(x, ...)

Arguments

x

A gosling object
...

further arguments passed to or from other methods.

Value

r list without NULL values

gosling render function

Description

gosling render function for shiny use

Usage

renderGosling(expr, env = parent.frame(), quoted = FALSE)

Arguments

expr

Expression returning the HTML / 'React' to render.
env

Environment in which to evaluate expr.
quoted

Is expr a quoted expression?

Value

A function which can be assigned to an output in a Shiny server function.

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)

}

Runs a shiny.gosling example

Description

Runs a shiny.gosling example

Usage

run_example(example = NA)

Arguments

example

A character indicating a valid example.

Value

A Shiny App is launched.

Examples

if (interactive()) {
  run_example("circularLinearWithBrush")
}

Data object builder

Description

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.

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.

Value

list of data specs

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)
}

Data object builder for a csv file

Description

Build the data object for gosling plots

Usage

track_data_csv(
  file,
  genomicFields = NULL,
  chromosomeField = NULL,
  separator = ",",
  sampleLength = 1000,
  headerNames = NULL,
  ...
)

Arguments

file

A character. Specify the URL address or local file name in the www directory of the data file.
genomicFields

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

A character. Specify the name of chromosome data fields.
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.
...

Any other parameters passed to json data object.

Value

list of data specs for a csv file

Examples

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

url <- "https://rb.gy/7y3fx"
temp_file <- file.path(tempdir(), "GSM1295076_CBX6_BF_ChipSeq_mergedReps_peaks.bed.gz")
download.file(url, destfile = temp_file)
df <- read.delim(
  temp_file,
  header = FALSE,
  comment.char = "#"
)
gr <- GRanges(
  seqnames = df$V1,
  ranges = IRanges(df$V2, df$V3)
)

if (!dir.exists("data")) {
  dir.create("data")
}
utils::write.csv(gr, "data/ChipSeqPeaks.csv", row.names = FALSE)

ui <- fluidPage(
  use_gosling(clear_files = FALSE),
  goslingOutput("gosling_plot")
)

track_1 <- add_single_track(
  width = 800,
  height = 180,
  data = track_data_csv(
    "data/ChipSeqPeaks.csv", chromosomeField = "seqnames",
    genomicFields = c("start", "end")
  ),
  mark = "bar",
  x = visual_channel_x(
    field = "start", type = "genomic", axis = "bottom"
  ),
  xe = visual_channel_x(field = "end", type = "genomic"),
  y = visual_channel_y(
    field = "width", type = "quantitative", axis = "right"
  ),
  size = list(value = 5)
)

composed_view <- compose_view(
  layout = "linear",
  tracks = track_1
)

arranged_view <- arrange_views(
  title = "Basic Marks: bar",
  subtitle = "Tutorial Examples",
  views = composed_view
)

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

shiny::shinyApp(ui, server)
}

Data object builder for a GRanges object by locally saving it

Description

Build the data object for gosling plots

Usage

track_data_gr(
  granges,
  chromosomeField = NULL,
  genomicFields = NULL,
  separator = ",",
  sampleLength = 1000,
  headerNames = NULL,
  ...
)

Arguments

granges

A GRanges object from the GenomicRanges package with seqnames and ranges
chromosomeField

A character. Specify the name of chromosome data fields.
genomicFields

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

Any other parameters passed to json data object.

Value

list of data specs for a csv file

Examples

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

url <- "https://rb.gy/7y3fx"
temp_file <- file.path(tempdir(), "GSM1295076_CBX6_BF_ChipSeq_mergedReps_peaks.bed.gz")
download.file(url, destfile = temp_file)
df <- read.delim(
  temp_file,
  header = FALSE,
  comment.char = "#"
)
gr <- GRanges(
  seqnames = df$V1,
  ranges = IRanges(df$V2, df$V3)
)

ui <- fluidPage(
  use_gosling(clear_files = FALSE),
  goslingOutput("gosling_plot")
)

track_1 <- add_single_track(
  width = 800,
  height = 180,
  data = track_data_gr(
    gr, chromosomeField = "seqnames",
    genomicFields = c("start", "end")
  ),
  mark = "bar",
  x = visual_channel_x(
    field = "start", type = "genomic", axis = "bottom"
  ),
  xe = visual_channel_x(field = "end", type = "genomic"),
  y = visual_channel_y(
    field = "width", type = "quantitative", axis = "right"
  ),
  size = list(value = 5)
)

composed_view <- compose_view(
  layout = "linear",
  tracks = track_1
)

arranged_view <- arrange_views(
  title = "Basic Marks: bar",
  subtitle = "Tutorial Examples",
  views = composed_view
)

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

shiny::shinyApp(ui, server)
}

Data transformer

Description

Do data transformations

Usage

track_data_transform(type = NULL, field = NULL, oneOf = NULL, not = NULL, ...)

Arguments

type

A character. One of "filter", "concat", "replace", "log", "displace", "exonSplit", "coverage", "genomicLength", "svType" and "subjson". Check usage details at http://gosling-lang.org/docs/data/#data-transform.
field

A character. filter is applied based on the values of the specified data field.
oneOf

A vector of characters or numbers. Check whether the value is an element in the provided list.
not

A Boolean. When "not": true, apply a NOT logical operation to the filter. Default: false.
...

Any other parameters to pass to gosling.js.

Details

For info visit http://gosling-lang.org/docs/data#data-transform There are multiple ways to transform data. Check documentation for details of usage.

Value

list of data transformations specs

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)
}

Combine multiple data transforms

Description

Combine multiple data transforms

Usage

track_data_transforms(...)

Arguments

...

Multiple data transform specs separated by comma.

Value

list of multiple data transform specs

Initiate gosling

Description

Add this function at the beginning of ui. This is needed for gosling to work in shiny plots.

Usage

use_gosling(clear_files = TRUE)

Arguments

clear_files

default FALSE. To clear the locally stored csv files created by gosling or not.

Value

Gosling initiator HTML.

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)
}

Generic visual channel builder

Description

Generic visual channel builder

Usage

visual_channel(field = NULL, type = NULL, range = NULL, domain = NULL, ...)

Arguments

field

A character. Name of the data field.
type

A character. Must be "genomic". Specify the data type.
range

A vector of characters or numbers. Values of the visual channel.
domain

A vector of characters or numbers. Values of the data.
...

Any other parameters to pass to gosling.js.

Details

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

Value

List object.

color visual channel

Description

color visual channel

Usage

visual_channel_color(
  field = NULL,
  title = NULL,
  type = NULL,
  scaleOffset = NULL,
  scale = 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).
scale

A character. One of "linear", "log".
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.

Details

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

Value

List object.

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)

}

opacity visual channel

Description

opacity visual channel

Usage

visual_channel_opacity(
  field = NULL,
  type = NULL,
  range = NULL,
  domain = NULL,
  ...
)

Arguments

field

A character. Name of the data field.
type

A character. Must be "genomic". Specify the data type.
range

A vector of characters or numbers. Values of the visual channel.
domain

A vector of characters or numbers. Values of the data.
...

Any other parameters to pass to gosling.js.

Details

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

Value

List object.

row visual channel

Description

row visual channel

Usage

visual_channel_row(
  field = NULL,
  type = NULL,
  padding = NULL,
  legend = NULL,
  grid = NULL,
  clip = NULL,
  axis = NULL,
  aggregate = NULL,
  ...
)

Arguments

field

A character. Name of the data field.
type

A character. Must be "genomic". Specify the data type.
padding

A number. Determines the size of inner white spaces on the top and bottom of individual rows. Default: 0.
legend

A Boolean. Whether to display legend. Default: FALSE.
grid

A Boolean. Whether to display grid. Default: FALSE.
clip

A Boolean. Clip row when the actual y value exceeds the max value of the y scale. Used only for bar marks at the moment. Default: TRUE.
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.

Details

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

Value

List object.

Examples

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

  # Circular track 1 ----
  circular_track1_data <- track_data(
    url = "https://server.gosling-lang.org/api/v1/tileset_info/?d=cistrome-multivec",
    type = "multivec",
    row = "sample",
    column = "position",
    value = "peak",
    categories = c("sample 1", "sample 2", "sample 3", "sample 4"),
    binSize = 4
  )

  circular_track1_x <- visual_channel_x(field = "start", type = "genomic")
  circular_track1_xe <- visual_channel_x(field = "end", type = "genomic")

  circular_track1_y <- visual_channel_y(field = "peak", type = "quantitative")

  circular_track1_row <- visual_channel_row(
    field = "sample", type = "nominal"
  )

  circular_track1_color <- visual_channel_color(
    field = "sample", type = "nominal"
  )

  circular_track1_tracks <- add_multi_tracks(
    add_single_track(
      mark = "bar"
    ),
    add_single_track(
      mark = "brush",
      x = visual_channel_x(linkingId = "detail-1"),
      color = "blue"
    ),
    add_single_track(
      mark = "brush",
      x = visual_channel_x(linkingId = "detail-2"),
      color = "red"
    )
  )

  circular_track1_styles <- default_track_styles(
    outlineWidth = 0
  )

  circular_track1 <- add_single_track(
    id = "circular_track1", alignment = "overlay", data = circular_track1_data,
    x = circular_track1_x, xe = circular_track1_xe,
    y = circular_track1_y, row = circular_track1_row,
    color = circular_track1_color,
    stroke =  "black", strokeWidth = 0.3,
    tracks = circular_track1_tracks,
    style = circular_track1_styles,
    width = 500, height = 100
  )

  # Compose Circular track ----
  circular_composed_view <- compose_view(
    multi = TRUE,
    tracks = add_multi_tracks(
      circular_track1
    ),
    static = TRUE, layout = "circular", alignment = "stack"
  )

  # Arrange final view
  circular_linear_view <- arrange_views(
    arrangement = "horizontal",
    views = list(circular_composed_view)
  )




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


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

  shinyApp(ui, server)

}

size visual channel

Description

size visual channel

Usage

visual_channel_size(
  field = NULL,
  type = NULL,
  range = NULL,
  domain = NULL,
  ...
)

Arguments

field

A character. Name of the data field.
type

A character. Must be "genomic". Specify the data type.
range

A vector of characters or numbers. Values of the visual channel. Range to be specified like range = c(min_size, max_size)
domain

A vector of characters or numbers. Values of the data.
...

Any other parameters to pass to gosling.js.

Details

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

Value

List object.

stroke visual channel

Description

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.

Details

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

Value

List object.

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)

}

stroke width visual channel

Description

stroke width visual channel

Usage

visual_channel_stroke_width(
  field = NULL,
  type = NULL,
  range = NULL,
  domain = NULL,
  ...
)

Arguments

field

A character. Name of the data field.
type

A character. Must be "genomic". Specify the data type.
range

A vector of characters or numbers. Values of the visual channel.
domain

A vector of characters or numbers. Values of the data.
...

Any other parameters to pass to gosling.js.

Details

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

Value

List object.

text visual channel

Description

text visual channel

Usage

visual_channel_text(
  field = NULL,
  type = NULL,
  range = NULL,
  domain = NULL,
  ...
)

Arguments

field

A character. Name of the data field.
type

A character. Must be "genomic". Specify the data type.
range

A vector of characters or numbers. Values of the visual channel.
domain

A vector of characters or numbers. Values of the data.
...

Any other parameters to pass to gosling.js.

Details

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

Value

List object.

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)

}

tooltip visual channel

Description

tooltip visual channel

Usage

visual_channel_tooltip(field = NULL, type = NULL, alt = NULL, ...)

Arguments

field

A character. Name of the data field.
type

A character. Must be "genomic". Specify the data type.
alt

A character.
...

Any other parameters to pass to gosling.js.

Details

For more info visit https://gosling.js.org/ and check for tooltip implementation

Value

List object. list object with tooltip 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_pdf",
          "PDF",
          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_pdf, {
      export_pdf(component_id = "component_1")
    })
  }

  shinyApp(ui, server)

}

Combine tooltips into a list

Description

Combine tooltips into a list

Usage

visual_channel_tooltips(...)

Arguments

...

Any other parameters to pass to gosling.js.

Value

List object. json list with tooltips combined into a single spec

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_pdf",
          "PDF",
          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_pdf, {
      export_pdf(component_id = "component_1")
    })
  }

  shinyApp(ui, server)

}

x and xe axis visual channel

Description

x and xe axis visual channel

Usage

visual_channel_x(
  field = NULL,
  type = NULL,
  legend = NULL,
  grid = NULL,
  axis = NULL,
  aggregate = NULL,
  ...
)

Arguments

field

A character. Name of the data field.
type

A character. Must be "genomic". Specify the data type.
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.

Details

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

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_pdf",
          "PDF",
          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_pdf, {
      export_pdf(component_id = "component_1")
    })
  }

  shinyApp(ui, server)

}

y and ye axis visual channel

Description

y and ye axis visual channel

Usage

visual_channel_y(
  field = NULL,
  zeroBaseline = NULL,
  type = NULL,
  legend = NULL,
  grid = NULL,
  flip = NULL,
  baseline = NULL,
  axis = NULL,
  aggregate = NULL,
  ...
)

Arguments

field

A character. Name of the data field.
zeroBaseline

A Boolean. Specify whether to use zero baseline. Default: TRUE.
type

A character. Must be "genomic". Specify the data type.
legend

A Boolean. Whether to display legend. Default: FALSE.
grid

A Boolean. Whether to display grid. Default: FALSE.
flip

A Boolean. Whether to flip the y-axis. This is done by inverting the range property. Default: FALSE.
baseline

A character or number. Custom baseline of the y-axis. Default: 0.
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.

Details

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

Value

List object.

Examples

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

  # Circular track 1 ----
  circular_track1_data <- track_data(
    url = "https://server.gosling-lang.org/api/v1/tileset_info/?d=cistrome-multivec",
    type = "multivec",
    row = "sample",
    column = "position",
    value = "peak",
    categories = c("sample 1", "sample 2", "sample 3", "sample 4"),
    binSize = 4
  )

  circular_track1_x <- visual_channel_x(field = "start", type = "genomic")
  circular_track1_xe <- visual_channel_x(field = "end", type = "genomic")

  circular_track1_y <- visual_channel_y(field = "peak", type = "quantitative")

  circular_track1_row <- visual_channel_row(
    field = "sample", type = "nominal"
  )

  circular_track1_color <- visual_channel_color(
    field = "sample", type = "nominal"
  )

  circular_track1_tracks <- add_multi_tracks(
    add_single_track(
      mark = "bar"
    ),
    add_single_track(
      mark = "brush",
      x = visual_channel_x(linkingId = "detail-1"),
      color = "blue"
    ),
    add_single_track(
      mark = "brush",
      x = visual_channel_x(linkingId = "detail-2"),
      color = "red"
    )
  )

  circular_track1_styles <- default_track_styles(
    outlineWidth = 0
  )

  circular_track1 <- add_single_track(
    id = "circular_track1", alignment = "overlay", data = circular_track1_data,
    x = circular_track1_x, xe = circular_track1_xe,
    y = circular_track1_y, row = circular_track1_row,
    color = circular_track1_color,
    stroke =  "black", strokeWidth = 0.3,
    tracks = circular_track1_tracks,
    style = circular_track1_styles,
    width = 500, height = 100
  )

  # Compose Circular track ----
  circular_composed_view <- compose_view(
    multi = TRUE,
    tracks = add_multi_tracks(
      circular_track1
    ),
    static = TRUE, layout = "circular", alignment = "stack"
  )

  # Arrange final view
  circular_linear_view <- arrange_views(
    arrangement = "horizontal",
    views = list(circular_composed_view)
  )




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


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

  shinyApp(ui, server)

}

Zoom to

Description

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)

}

Zoom to extent

Description

Zooms out to see the entire view_id passed to this function.

Usage

zoom_to_extent(
  component_id,
  view_id,
  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.
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)

  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 Out"
        )
      )
    )
  )


  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_extent(
        component_id = "component_1",
        view_id = "track1"
      )
    })
  }

  shinyApp(ui, server)

}