17 July 2019

I really like how easy it is to modify the simple inputs in shiny. For example last week I had to make three sets of checkboxGroupInputs, all with the same choices, to control which visuals would appear in a markdown report. My first draft had three distinct inputs, but this was not space efficient and felt completely inelegant. making a table of selections seemed like a much better idea, but of course no such input exists natively in shiny.

Making an input like this is really simple:

Gene Symbol Lollipop Plot Boxplot Histogram

This is a dynamic input, so it is rendered on the server and then displayed. Here is the server code:

# This would be a reactive that gathers the values from the ui somehow
selectedGene <- function() {
	c("NOTCH1", "EGFR", "TPTE", "TP53", "KRAS", "BRCA1", "BRCA2")

# Render the table of genes
output$geneselectiontable <- renderUI({
	genes <- selectedGene()
	trows <- unlist(lapply(genes, function(x) {
			  <td style="padding:0px 8px;">', x, '</td>
			  <td class="checkbox">', tags$input(type="checkbox", name="reportlolliplots", value=x), '</td>
			  <td class="checkbox">', tags$input(type="checkbox", name="reportboxplots", value=x), '</td>
			  <td class="checkbox">', tags$input(type="checkbox", name="reporthistograms", value=x), '</td>

	tab <- paste0('
		<table id="', "reportgenegrouptable), '">
			<th>Gene Symbol</th>
			<th>Lollipop Plot</th>
		  </tr></thead>' ,
		  paste(trows, collapse=" "), '
	div(id="reportlolliplots", class="form-group shiny-input-checkboxgroup shiny-input-container",
		div(id="reportboxplots", class="form-group shiny-input-checkboxgroup shiny-input-container",
			div(id="reporthistograms", class="form-group shiny-input-checkboxgroup shiny-input-container",

Of course the updateCheckboxGroupInput function no longer works on this table, so we have to modify it a little bit. The reason it no longer works is because it locates the div, clears it, then recreates it, potentially with different choices. Since my table is rendered my update function does not need to add or remove choices – it only needs to check and un-check the boxes.

The simplest way to do this is to use a custom message handler. Here’s mine, that I source in as a script in my ui:

  function(message) {
    // Copied verbatim from shiny.js
    // Escape jQuery selector metacharacters: !"#$%&'()*+,./:;<=>?@[\]^`{|}~
    var exports = window.Shiny = window.Shiny || {};
    var $escape = exports.$escape = function(val) {
      return val.replace(/([!"#$%&'()*+,.\/:;<=>?@\[\\\]^`{|}~])/g, '\\$1');
    // Adapted from shiny.js
    var el = $(message.id + '.shiny-input-checkboxgroup');
    // Clear all checkboxes
    $('input:checkbox[name="' + $escape(message.id) + '"]').prop('checked', false);
    var value = message.value;
    // Accept array
    if (value instanceof Array) {
      for (var i = 0; i < value.length; i++) {
        $('input:checkbox[name="' + $escape(message.id) + '"][value="' + $escape(value[i]) + '"]')
          .prop('checked', true);
    // Else assume it's a single value
    } else {
      $('input:checkbox[name="' + $escape(message.id) + '"][value="' + $escape(value) + '"]')
        .prop('checked', true);


To use it I collect the choices I want to check and uncheck, and pass them to the messageHandler:

# Update which expression plots to include
	# This makes sure we can't run until the first gene selections are made
	genes <- selectedGene()
		if(length(genes)) {
			boxplotsalreadyselected <- reportGenes$boxplots
			if(length(boxplotsalreadyselected)) session$sendCustomMessage("updateCheckGroup", message=list(id="reportboxplots", value=boxplotsalreadyselected))
			histogramsalreadyselected <- reportGenes$histograms
			if(length(histogramsalreadyselected)) session$sendCustomMessage("updateCheckGroup", message=list(id="reporthistograms", value=histogramsalreadyselected))
			lolliplotsalreadyselected <- reportGenes$lolliplots
			if(length(lolliplotsalreadyselected)) session$sendCustomMessage("updateCheckGroup", message=list(id="reportlolliplots", value=lolliplotsalreadyselected))