A module to visualize a volcano plot. — mgVolcano • sparrow.shiny

Users can specify logFC and FDR thresholds for which the individual dots in the volcano are rather hexbins so that the browser doesn't have to handle a single point for each gene/dot.

mgVolcano(
  input,
  output,
  session,
  x,
  stats = "dge",
  xaxis = "logFC",
  yaxis = "pval",
  idx = "idx",
  tools = c("box_select", "reset", "save"),
  width = NULL,
  height = NULL,
  highlight = shiny::reactive(NULL),
  default_xhex = 1,
  default_yhex = 0.1,
  webgl = FALSE,
  ...
)

mgVolcanoUI(
  id,
  x,
  stats = "dge",
  xaxis = "logFC",
  yaxis = "padj",
  idx = "idx",
  hexbin = TRUE,
  default_xhex = 1,
  default_yhex = 0.1
)

Arguments

input, output, session: shiny bits
x: A SparrowResult object, or a data.frame
stats: One of "dge" or resultNames(x)
xaxis: the column of the the provided (or extracted) data.frame to use for the xaxis and yaxis of the volcano
yaxis: the column of the the provided (or extracted) data.frame to use for the xaxis and yaxis of the volcano
idx: The column of the data.frame to use as the identifier for the element in the row. You probably don't want to mess with this
tools: the plotly tools to include in the figures toolbar
width: the width and height of the output plotly plot
height: the width and height of the output plotly plot
highlight: a reactive vector of featureIds that indicate which points to highlight on the volcano, irresespective of their "hexbin" status.
default_xhex, default_yhex: default values to set the slider inputs to pass in for hex-ization
webgl: use webgl to make the plotly plot
...: pass through arguments (not used)
id: the shiny id of the output widget
hexbin: boolean to indicate if the UI should show a wrench widget to configure the parameters for the hexbin drawing (default: `TRUE`)

Value

A reactive data.frame that includes the information of the genes that are brushed in the volcano plot. If no genes have been selected, then `NULL`.

Functions

mgVolcanoUI: the UI for the module

Examples

sres <- sparrow::exampleSparrowResult()
app <- shiny::shinyApp(
  ui = shiny::shinyUI(shiny::fluidPage(
    exampleUISetup(),
    title = "Interactive volcano plot",
    mgVolcanoUI("mod"))),
  server = function(input, output, session) {
    src <- shiny::reactive(SparrowResultContainer(sres))
    shiny::callModule(mgVolcano, "mod", src, default_xhex = 2)
  })
if (interactive()) {
  shiny::runApp(app)
}