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Create an example Modular ComplexHeatmap Shiny Application

Source: R/ComplexHeatmap_Heatmap_module_app.R
ComplexHeatmap_HeatmapApp.Rd

This function generates a Shiny application with modular ComplexHeatmap::Heatmap() components rendered interactively via InteractiveComplexHeatmap. The app features a Data Import section for uploading data, a Data Table for filtering the active dataset, and a Plot area for configuring and displaying the interactive heatmap.

Usage

ComplexHeatmap_HeatmapApp(
  data_list = NULL,
  column_data = NULL,
  defaults = NULL,
  hide.inputs = NULL,
  hide.tabs = NULL
)

Arguments

data_list

An optional named list of data frames. If NULL (the default), list("matrix" = example_heatmap_matrix) is used as example data. Ignored (only its first element is used, as the matrix) when column_data is supplied — that path has no dataset picker/upload/filter UI.

column_data

An optional data frame of per-sample metadata, enabling column annotations (see ComplexHeatmap_HeatmapServer()'s data parameter for the expected shape — a key column matching the matrix's column names, plus arbitrary annotation columns). When supplied, the app is a minimal single-dataset shinyApp() (no Data Import/Data Table sections) wiring data = list(matrix = <first element of data_list, or example_heatmap_matrix>, column_annotations = column_data) directly into the module.

defaults

A named list of input IDs and their default values to apply on startup. An entry may also be a shiny::reactive() or shiny::reactiveVal() to have the input follow the parent app's state; see setup_reactive_defaults().

hide.inputs

A character vector of input IDs to hide. Their values are still initialized and used, but the controls are not shown in the UI.

hide.tabs

A character vector of tab names to hide. Inputs in these tabs are still initialized and used, but the controls are not shown in the UI.

Value

A Shiny app object.

Details

When data_list is not provided (or NULL), the app launches with example_heatmap_matrix (a simulated gene x sample expression matrix) as an example dataset. Uploaded data files are added to the available datasets and can be selected for plotting. If an uploaded file shares a name with an existing dataset, the existing one is overwritten with a warning.

Unlike the other modules, this one depends on the Bioconductor packages ComplexHeatmap, InteractiveComplexHeatmap, and circlize, which must be installed (e.g. via BiocManager::install()).

This is a convenience wrapper around createModuleApp() — except when column_data is supplied (see below), which needs a small bespoke app instead, since createModuleApp() always hands the module server a single data frame and can't carry the two-table list(matrix = , column_annotations = ) shape the module's column-annotation feature needs (see ComplexHeatmap_HeatmapServer()'s data parameter).

See also

ComplexHeatmap::Heatmap(), ComplexHeatmap_HeatmapInputsUI(), ComplexHeatmap_HeatmapOutputUI(), ComplexHeatmap_HeatmapServer()

Author

Jacob Martin, Jared Andrews

Examples

library(VizModules)
# Launch with default example data (row annotations only):
app <- ComplexHeatmap_HeatmapApp()
if (interactive()) shiny::runApp(app)

# Launch with column annotations too:
app2 <- ComplexHeatmap_HeatmapApp(column_data = example_heatmap_column_data)
if (interactive()) shiny::runApp(app2)