Overview

picker lets you zoom, pan, and pick points from a scatter plot.

Installation

# install.packages("remotes")
remotes::install_github("hms-dbmi/picker")

Usage

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()

if (require(repel)) {
    # repel labels
    label_coords$label <- levels(labels)[as.numeric(label_coords$label)]
    label_coords <- repel_text(label_coords, mar = rep(0, 4), fontsize = 16)
    
    # adjust text props to be the same
    text_props$getSize <- 16
    text_props$getTextAnchor <- 'middle'
    text_props$getAlignmentBaseline <- 'center'
    
} else {
    message("See https://github.com/hms-dbmi/repel to install repel")
}

# 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 = '↑'),
    list(color = '#0000FF', label = '↓'),
    list(color = '#989898', label = 'p < .05'),
    list(color = '#EAEAEA', label = 'p ≥ .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, 'Δ 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))

Development

cd javascript
npm run build