selectmatrix: The server function of the selectmatrix module

In pinin4fjords/shinyngs: Shiny apps for NGS data

The server function of the selectmatrix module

Description

This module forms the core of many operations in shinyngs. To use the matrix data stored in an ExploratorySummarizedExperimentList object, selection must be made on the basis of experiment (which ExploratorySummarizedExperiment) to use), the specific assay of the experiment, and the rows and columns of the selected assay matrix. This module provides customisable controls for selection at each of these levels, and parses those inputs to produce matrices used in the various plots.

Usage

selectmatrix(
  input,
  output,
  session,
  eselist,
  var_n = 50,
  var_max = NULL,
  select_assays = TRUE,
  select_samples = TRUE,
  select_genes = TRUE,
  provide_all_genes = FALSE,
  default_gene_select = NULL,
  require_contrast_stats = FALSE,
  rounding = 2,
  select_meta = TRUE,
  allow_summarise = TRUE
)

Arguments

input	Input object
output	Output object
session	Session object
eselist	ExploratorySummarizedExperimentList object containing ExploratorySummarizedExperiment objects
var_n	The number of rows to select when doing so by variance. Default = 50
var_max	The maximum umber of rows to select when doing so by variance. Default = 500
select_assays	Provide UI and functions for assay selection?
select_samples	Provide UI and functions for sample selection? (Default: TRUE)
select_genes	Provide UI and functions for gene (row) selection? (Default: TRUE)
provide_all_genes	Allow the 'all rows' selection in the UI? Means we don't have to calculate variance so the display is quicker, but it's a bad idea for e.g. heatmaps where the visual scales by the numbre of rows.
default_gene_select	The default method to use for selecting genes
require_contrast_stats	Only use elements of eselist that have a populated contrast_stats slot. For plots using p value data etc, this is used to hide experiments that don't have the necessary data.
rounding	Number of decimal places to show in results (Default 2)
select_meta	Boolean- add metadata controls?
allow_summarise	Boolean, show controls for matrix summarisation?

Details

The geneselect and sampleselect modules provide row- and column- selection, respectively. This will generally not be called directly, but by other modules such as the heatmap module.

This function is not called directly, but rather via callModule() (see example).

Value

output A list of reactive functions for fetching the derived matrix and making a title based on its properties.

Examples

selectSamples <- callModule(sampleselect, "selectmatrix", eselist)

pinin4fjords/shinyngs documentation built on Jan. 18, 2025, 7:09 p.m.