tmodBrowserTableServer: Shiny Module – tmod results browser table selection

In bihealth/bioshmods: What the Package Does (One Line, Title Case)

Shiny Module – tmod results browser table selection

Description

Shiny Module – tmod results browser table selection

Usage

tmodBrowserTableUI(id, cntr_titles, upset_pane = FALSE)

tmodBrowserTableServer(
  id,
  tmod_res,
  gs_id = NULL,
  multilevel = FALSE,
  tmod_dbs = NULL
)

Arguments

id	identifier for the namespace of the module
cntr_titles	possibly named character vector with contrast names
upset_pane	if TRUE, UI for the upset plot will be created
tmod_res	results of tmod analysis. It is a list of lists of lists of data frames. See Details.
gs_id	a list of reactive values (returned by shiny::reactiveValues()), including dataset (ds), gene set ID (id), contrast id (cntr), database ID (db) and sorting mode (sort). If mod_id is not NULL, these reactive values will be populated, possibly triggering an action in another shiny module.
multilevel	if TRUE, the results are grouped in data sets
tmod_dbs	(optional) list of tmod database objects (or lists of list of tmod database object in multi data set mode). If NULL, upset plots cannot be generated. See Details.

Details

Regarding required data, this is probably the most complex module. That is due to the complexity of gene set enrichment analysis – we can test gene set enrichment using different parameters (e.g. gene list sorting order), for different gene set collections (such as KEGG or Hallmark from MSigDB) and, of course, for different contrast.

This module is adapted to gene set enrichment testing using the tmod package (described in Zyla et al. 2019).

Use of tmod database objects

For gene set enrichments, collections (databases) of gene sets must be defined. Such gene set collections include KEGG and REACTOME pathways, Gene Ontologies, transcriptional modules as well as meta-collections such as MSigDB.

There are many ways of storing such gene set collections. One way that I find convenient (since I programmed it myself) is included in the gene set enrichment testing package tmod. Tmod database objects are lists with at least three elements: gs, gv and gv2gs (see details in the tmod package). They can be conveniently created using the tmod package.

In 'bioshmods', these objects are included in a structure which provides gene set information to the 'bioshmods' functions. Each such structure is a named list with one element per gene set collection (i.e., if you have gene set enrichment results for KEGG and REACTOME, you will have two such elements). Each of these element is a tmod database object (returned, for example, by the tmod::makeTmod() function from the 'tmod' package). See the example dataset C19_gs.

Gene set enrichment analysis results

This object needs to be a hierarchical lists of lists of lists. Top list is a named list, with each element corresponding to one contrast. On the next level, there is a named element for each gene set collection (see 'Use of tmod objects'). Finally, there may be different sorting options (if in doubt, use pval as the only element). The lowest level are data frames containing column 'ID', 'Title', 'AUC', 'P.Value' and 'adj.P.Val' as returned by e.g. tmod::tmodCERNOtest().

Examples

## Building an example from scratch
data(C19)
data(C19_gs)

db <- C19_gs$tmod_dbs$tmod

ds_res <- C19$contrasts$COVID19_ID0

ds_res <- ds_res[ order(ds_res$pvalue), ]

library(tmod)
tmod_res <- tmodCERNOtest(ds_res$symbol, mset=db)

# sorting by p-value
tmod_res <- list(pval=tmod_res)

# for datbase tmod
tmod_res <- list(tmod=tmod_res)

# for contrast Covid
tmod_res <- list(Covid=tmod_res)

if(interactive()) {

  ui <- fluidPage(tmodBrowserTableUI("tt", names(tmod_res)))
  server <- function(input, output) {
    tmodBrowserTableServer("tt", tmod_res)
  }
  shinyApp(ui, server)

}

## the data sets in `bioshmods` are preformatted, so we can use them
## directly.

if(interactive()) {

  ui <- fluidPage(tmodBrowserTableUI("tt", names(C19_gs$tmod_res), upset=TRUE))
  server <- function(input, output) {
    tmodBrowserTableServer("tt", C19_gs$tmod_res, gs_id = NULL,
                                 tmod_dbs = C19_gs$tmod_dbs)
  }
  shinyApp(ui, server)

}

bihealth/bioshmods documentation built on July 1, 2023, 4:32 a.m.