mgVolcano: A module to visualize a volcano plot.

In lianos/sparrow.shiny: Provides shiny modules to visualize sparrow results

A module to visualize a volcano plot.

Description

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.

Usage

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)
}

lianos/sparrow.shiny documentation built on Oct. 12, 2023, 2:43 a.m.