Bar plot of missing values per lines using highcharter.

Source: R/omXplore_view_dataset.R

This method plots a bar plot which represents the distribution of the number of missing values (NA) per lines (i.e. proteins).

view_dataset_ui(id)

view_dataset_server(
  id,
  obj = reactive({
     NULL
 }),
  addons = list(),
  useModal = TRUE,
  verbose = FALSE
)

view_dataset(obj = NULL, addons = NULL, useModal = TRUE)

Arguments

id

A character(1) for the 'id' of the shiny module. It must be the same as for the '*_ui' function.

obj

An instance of the class MultiAssayExperiment.

addons

A list to configure the other shiny apps to integrate. Each item correspond to one package:

  • the name of the slot is the name of the package

  • the content of the slot is a vector composed of the generic name of the shiny app. Each of the apps listed here must be an exported app of the package. For example, given the value addons = list(testPkg = c('foo', 'foo2')). That means that the package called "testPkg" must provide the four functions: foo1_ui(), foo1_server() and foo2_ui(), foo2_server())

useModal

A boolean(1) that indicates whether to open plot modules in a modal window or not. Default is TRUE.

verbose

A boolean for verbose mode. Default is FALSE.

Value

NA

NA

NA

A shiny application which wraps the functions view_dataset_ui() and the view_dataset_server()

Details

  • distribution of the missing values per line,

  • a bar plot which represents the distribution of the number of missing values (NA) per lines (i.e. proteins) and per conditions,

  • Histogram of missing values.

  • Variance : Builds a densityplot of the CV of entities in numeric matrix. The CV is calculated for each condition present in the dataset (see the slot 'Condition' in the colData() DataFrame)

  • Heatmap:

The function heatmapD()

The function [] is inspired from the function 'heatmap.2' that displays a numeric matrix. For more information, please refer to the help of the heatmap.2 function.

Missing values

#' - distribution of the missing values per line,

  • a bar plot which represents the distribution of the number of missing values (NA) per lines (ie proteins) and per conditions,

  • Histogram of missing values.

Author

Samuel Wieczorek, Enora Fremy

Examples

if (FALSE) { # \dontrun{
  data(vdata)
  addons <- list(omXplore = c("extFoo1", "extFoo2"))
  runApp(view_dataset(vdata, addons))
  
  shiny::runApp(view_dataset(vdata))
} # }


if (interactive()) {
  data(vdata)
  view_dataset(vdata)
}