Create an example Modular ComplexHeatmap Shiny Application

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), example_heatmap_matrix is used as example data — paired with example_heatmap_column_data unless column_data says otherwise. When column_data is supplied it is attached to the first entry, which becomes list(matrix = , column_annotations = ).
column_data: An optional data frame of per-sample metadata, enabling column annotations, column splitting, and metadata-aware column filtering. Defaults to example_heatmap_column_data when data_list is also NULL; pass data_list explicitly to opt out. Attached to the first data_list entry (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 neither data_list nor column_data is provided, the app launches on the bundled pair — example_heatmap_matrix (a simulated gene x sample expression matrix) together with example_heatmap_column_data (its per-sample metadata), with column_key seeded to "sample". The column-annotation, column-split, and column-filter features are all inert without a metadata table, so this way a bare ComplexHeatmap_HeatmapApp() demonstrates the whole module.

Either way the app has the usual Data Import section for uploading data and a Data Table for filtering the active dataset. Filtering applies to the matrix; any companion metadata table rides along untouched. 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(), which accepts a dataset entry that is a list of tables and filters only the primary one, so the two-table list(matrix = , column_annotations = ) shape this module's column features need is carried through without a bespoke app (see ComplexHeatmap_HeatmapServer()'s data parameter).

Author

Jacob Martin, Jared Andrews

Examples

library(VizModules)
# Launch on the bundled matrix + its per-sample metadata, so the column
# annotation/split/filter features are all usable:
app <- ComplexHeatmap_HeatmapApp()
if (interactive()) shiny::runApp(app)

# Matrix only, without the per-sample metadata:
app2 <- ComplexHeatmap_HeatmapApp(data_list = list(matrix = example_heatmap_matrix))
if (interactive()) shiny::runApp(app2)