discoServer: Shiny Module – disco plots

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

Shiny Module – disco plots

Description

Shiny Module – disco plots

Usage

discoUI(id, cntr_titles)

discoServer(
  id,
  cntr,
  annot = NULL,
  selcols = c("PrimaryID", "ENTREZ", "SYMBOL"),
  primary_id = "PrimaryID",
  gene_id = NULL
)

Arguments

id	identifier of the shiny module (character vector)
cntr_titles	character vector containing the IDs of the contrasts (same as names(cntr)).
cntr	list of data frames containing the contrast information. Data frames must have the columns log2FoldChange and pvalue. Rownames of the data frames should be IDs.
annot	Annotation data frame. The annotation data frame must have a column named "PrimaryID" which corresponds to the rownames of the data frames in the cntr list.
selcols	which column in the gene table when genes are selected from the plot
primary_id	name of the contrast data frame column with the primary IDs
gene_id	must be a reactiveValues object. If not NULL, then clicking on a gene identifier will modify this object (possibly triggering an event in another module).

Value

Returns a reactive expression returning the ID of the activated gene

Examples

if(interactive()) {
    cntr1 <- data.frame(log2FoldChange=rnorm(5000),
                        pvalue=runif(5000),
                        PrimaryID=paste0("ID", 1:5000))
    cntr2 <- data.frame(log2FoldChange=cntr1$log2FoldChange + 
                                       rnorm(5000),
                        pvalue=runif(5000) * cntr1$pvalue,
                        PrimaryID=paste0("ID", 1:5000))
    cntr1$SecondaryID <- sample(cntr1$PrimaryID, replace=TRUE)
    cntr2$SecondaryID <- sample(cntr2$PrimaryID, replace=TRUE)
    rownames(cntr2) <- paste0("ID", 1:5000)
    cntr <- list("Contrast 1"=cntr1, "Contrast 2"=cntr2)
    shinyApp(ui=fluidPage(discoUI("disco", names(cntr))),
             server=function(input, output, session) {
                discoServer("disco", cntr)
             })
}

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