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The server function of the contrasts module

Source: R/contrasts.R
contrasts.Rd

This module provides the form elements to control contrasts used in e.g. differential expression panels. In particular it provides the ability for users to add filters to progressively refine a query.

Usage

contrasts(
  id,
  eselist,
  selectmatrix_reactives = list(),
  multiple = FALSE,
  select_all_contrasts = FALSE,
  show_controls = TRUE,
  default_foldchange = 2,
  default_pval = 0.05,
  default_qval = 0.1
)

Arguments

id

Module namespace

eselist

ExploratorySummarizedExperimentList object containing ExploratorySummarizedExperiment objects

selectmatrix_reactives

The list of reactive expressions returned by a call to the selectmatrix module. This will be unpacked to gain access to the data provided by those reaactive.

multiple

Allow selection of multiple contrasts?

select_all_contrasts

Select all contrasts by default?

show_controls

Show the controls for contrast selection?

default_foldchange

default value for the fold change filter

default_pval

Default value for the p value field

default_qval

Default value for the q value field

Details

This function is called directly, using the same id as its UI counterpart, and wraps its logic in moduleServer() (see example).

The reactive graph is built by a sequence of internal factory functions, each owning one cohesive stage (contrast enumeration, naming, the dynamic filter-set engine, table building, selection, filtering, labelling, and the query summary) - see contrastEnumeration, contrastNaming, contrastFilterSetEngine, contrastTableBuilder, contrastSelection, contrastFiltering, contrastLabelling and contrastQuerySummary. This function itself just wires those stages together in dependency order and returns their public reactives.

Examples

contrasts("differential", eselist = eselist, selectmatrix_reactives = selectmatrix_reactives, multiple = TRUE)
#> Error in contrasts("differential", eselist = eselist, selectmatrix_reactives = selectmatrix_reactives,     multiple = TRUE): unused arguments (eselist = eselist, selectmatrix_reactives = selectmatrix_reactives, multiple = TRUE)