Title: Pick Data Points from a Deck.gl Scatterplot
Version: 0.2.6
Description: Performant interactive scatterplot for ~ 1 million points. Zoom, pan, and pick points. Includes tooltips, labels, a grid overlay, legend, and coupled interactions across multiple plots.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.1.2
URL: https://github.com/hms-dbmi/picker
BugReports: https://github.com/hms-dbmi/picker/issues
Imports: htmlwidgets (≥ 1.5.3)
Suggests: shiny, scales
Depends: R (≥ 4.0)
NeedsCompilation: no
Packaged: 2022-03-30 17:26:11 UTC; alex
Author: Alex Pickering [aut, cre]
Maintainer: Alex Pickering <alexvpickering@gmail.com>
Repository: CRAN
Date/Publication: 2022-03-31 07:30:07 UTC

Render a Picker Widget

Description

Render a Picker Widget

Usage

picker(
  coords,
  colors,
  labels,
  title = NULL,
  label_coords = NULL,
  polygons = NULL,
  point_color_polygons = NULL,
  show_controls = TRUE,
  grid_legend_items = NULL,
  scale_legend_props = NULL,
  scatter_props = NULL,
  deck_props = NULL,
  text_props = NULL,
  polygon_props = NULL,
  xrange = NULL,
  yrange = NULL,
  xaxs = 0.04,
  yaxs = 0.04,
  width = NULL,
  height = NULL,
  elementId = NULL
)

Arguments

coords

data.frame with two columns. First has x, second has y coordinates.

colors

vector of hex colors, one for each row of coords.

labels

vector of point labels used for tooltips on hover.

title

character string to show in top left of plot.

label_coords

data.frame with three columns 'x', 'y', and 'label'. Used for text layer.

polygons

data.frame containing at minimum columns 'x1', 'x2', 'y1', 'y2', that define the polygons to draw and 'color' that defines the color.

point_color_polygons

character, a color to make points when polygons are shown e.g. 'white'.

show_controls

Should control panel be shown? Default is TRUE.

grid_legend_items

list of lists with color hex for legend square and label for legend items. Only visible for grid display.

scale_legend_props

optional props to render a gradient scale legend. For example: list(colorHigh = 'red', colorLow = 'gray', high = 4, low = 0)

scatter_props

Props passed to deck.gl ScatterplotLayer.

deck_props

Props passed to deck.gl Deck instance.

text_props

Props passed to deck.gl TextLayer.

polygon_props

Props passed to deck.gl PolygonLayer.

xrange

range of x-values. Default is range(coords[,1]).

yrange

range of y-values. Default is range(coords[,2]).

xaxs

the fraction to extend xrange on either side. Default is 0.04.

yaxs

the fraction to extend yrange on either side. Default is 0.04.

width

width of htmlwidget.

height

height of htmlwidget.

elementId

id of htmlwidget.

Value

renders html widget

Examples


if (interactive()) {
  library(shiny)
  library(picker)

  # load example data
  load(system.file('extdata/pbmcs.rda', package = 'picker'))

  # setup gradient scale legend
  scale_legend_props <- list(
    colorHigh = 'blue',
    colorLow = '#f5f5f5',
    high = round(max(exp)),
    low = min(exp))

  text_props <- list()

  # get colors for gene expression
  exp <- scales::rescale(exp, c(0, 1))
  expression_colors <- scales::seq_gradient_pal('#f5f5f5', 'blue')(exp)

  # legend to show when grid is visible
  grid_legend_items = list(
    list(color = '#FF0000', label = '\U2191'),
    list(color = '#0000FF', label = '\U2193'),
    list(color = '#989898', label = 'p \U003C .05'),
    list(color = '#EAEAEA', label = 'p \U2265 .05')
  )

  ui = shinyUI(fluidPage(
    tags$head(tags$style(".picker {border: 1px solid #ddd; margin: 20px 0;}")),
    shiny::column(
      width = 6,
      pickerOutput('clusters', width = '100%', height = '400px'),
      pickerOutput('expression', width = '100%', height = '400px'),
      verbatimTextOutput('selected')
    )
  ))

  server = function(input, output) {

    # show selected output
    output$selected <- renderPrint({
      input$clusters_selected_points
    })

    # coordinate views (zoom/pan)
    clusters_proxy <- picker_proxy('clusters')
    observeEvent(input$expression_view_state, {
      update_picker(clusters_proxy, input$expression_view_state)
    })

    expression_proxy <- picker_proxy('expression')
    observeEvent(input$clusters_view_state, {
      update_picker(expression_proxy, input$clusters_view_state)
    })

    # change title between grid/scatterplot
    observeEvent(input$clusters_show_grid, {
      title <- ifelse(input$clusters_show_grid, '\U0394 CELLS', '')
      update_picker(clusters_proxy, title = title)
    })


    # render pickers
    output$clusters <- renderPicker(
      picker(
        coords,
        cluster_colors,
        labels,
        label_coords = label_coords,
        polygons = polygons,
        text_props = text_props,
        point_color_polygons = 'white',
        grid_legend_items = grid_legend_items)
    )

    output$expression <- renderPicker(
      picker(coords,
             expression_colors,
             labels,
             show_controls = FALSE,
             scale_legend_props = scale_legend_props)
    )
  }

  shinyApp(ui = ui, server = server, options = list(launch.browser = TRUE))
}

Shiny bindings for picker

Description

Output and render functions for using picker within Shiny applications and interactive Rmd documents.

Usage

pickerOutput(outputId, width = "100%", height = "400px")

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

Arguments

outputId

output variable to read from

width, height

Must be a valid CSS unit (like '100%', '400px', 'auto') or a number, which will be coerced to a string and have 'px' appended.

expr

An expression that generates a picker

env

The environment in which to evaluate expr.

quoted

Is expr a quoted expression (with quote())? This is useful if you want to save an expression in a variable.

Value

An output or render function that enables the use of the widget within Shiny applications.

Create a picker proxy object

Description

Creates a picker-like object that can be used to update a picker object that has already been rendered.

Usage

picker_proxy(shinyId, session = shiny::getDefaultReactiveDomain())

Arguments

shinyId

single-element character vector indicating the output ID of the deck to modify

session

the Shiny session object to which the picker widget belongs; usually the default value will suffice.

Value

a picker_proxy object that can be updated with update_picker.

See Also

update_picker

Send commands to a picker instance in a Shiny app

Description

Send commands to a picker instance in a Shiny app

Usage

update_picker(
  proxy,
  view_state = NULL,
  colors = NULL,
  labels = NULL,
  label_coords = NULL,
  polygons = NULL,
  show_grid = NULL,
  title = NULL
)

Arguments

proxy

picker proxy object created by picker_proxy.

view_state

view state from other picker input (optional).

colors

vector of hex colors, one for each row of coords.

labels

vector of point labels used for tooltips on hover.

label_coords

data.frame with three columns 'x', 'y', and 'label'. Used for text layer.

polygons

data.frame containing at minimum columns 'x1', 'x2', 'y1', 'y2', that define the polygons to draw and 'color' that defines the color.

show_grid

set to TRUE to turn on grid layer.

title

character string to show in top left of plot.

Value

The original proxy object. Called for side effects.

See Also

picker_proxy