Distilled enrichment map module

UI & module to generate distill enrichment map plots.

Usage

distillPlotUI(id, panel)

distillPlotServer(id, obj, args, config)

Arguments

id

Module id

panel

string, can be 'sidebar' or 'main'

obj

reactive containing 'distilled' enrichment results

args

reactive, list with plot arguments, 'numcat' (number of categories to plot)

config

reactive list with config settings

Value

UI returns tagList with plot UI server returns reactive with number of plotted terms

Examples

library(GeneTonic)
#> Welcome to GeneTonic v3.0.0
#> 
#> If you use GeneTonic in your work, please cite:
#> 
#>   GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
#>   Federico Marini, Annekathrin Ludt, Jan Linke, Konstantin Strauch
#>   BMC Bioinformatics, 2021 - https://doi.org/10.1186/s12859-021-04461-5
#> and/or (if adopting the series of protocols as a whole)
#>   Interactive and Reproducible Workflows for Exploring and Modeling RNA-seq Data with pcaExplorer, ideal, and GeneTonic
#>   Annekathrin Ludt, Arsenij Ustjanzew, Harald Binder, Konstantin Strauch, Federico Marini
#>   Current Protocols, 2022 - https://doi.org/10.1002/cpz1.411
#> 
#> Attaching package: ‘GeneTonic’
#> The following object is masked from ‘package:carnation’:
#> 
#>     gs_radar
library(shiny)

# get DESeqResults object
data(res_dex, package='carnation')

# get enrichResult object
data(eres_dex, package='carnation')

# preprocess & convert to GeneTonic object
eres2 <- GeneTonic::shake_enrichResult(eres_dex)
#> Found 2483 gene sets in `enrichResult` object, of which 2483 are significant.
#> Converting for usage in GeneTonic...
gt <- enrich_to_genetonic(eres_dex, res_dex)
#> Found 2483 gene sets in `enrichResult` object, of which 2483 are significant.
#> Converting for usage in GeneTonic...

# get distilled results
df <- distill_enrichment(
        eres2,
        res_dex,
        gt$anno_df,
        n_gs = 10,
        cluster_fun = "cluster_markov"
      )

# number of plotted terms
args <- reactive({ list(numcat=10) })

config <- reactiveVal(get_config())

# run simple shiny app with plot
if(interactive()){
  shinyApp(
    ui = fluidPage(
           sidebarPanel(distillPlotUI('p', 'sidebar')),
           mainPanel(distillPlotUI('p', 'main'))
         ),
    server = function(input, output, session){
               numcat <- observe({
                 distillPlotServer('p',
                                   reactive({ df }),
                                   args,
                                   config)
               })
             }
  )
}