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Heatmap module

Source: R/heatmap.R
heatmapmod.Rd

Module UI & server to generate heatmap.

Usage

heatmapUI(id, panel)

heatmapServer(id, obj, coldata, plot_args, gene_scratchpad, config)

Arguments

id

Module id

panel

string, can be 'sidebar' or 'main'

obj

reactiveValues object containing carnation object

coldata

reactiveValues object containing object metadata

plot_args

reactive containing 'fdr.thres' (padj threshold), 'fc.thres' (log2FC) & 'upset_data' (list containing data from upset plot module)

gene_scratchpad

reactiveValues object containing genes selected in scratchpad which will be labeled

config

reactive list with config settings

Value

UI returns tagList with heatmap UI. Server invisibly returns NULL (used for side effects).

Examples

if (FALSE) { # interactive()
library(shiny)
library(DESeq2)

# Create reactive values to simulate app state
oobj <- make_example_carnation_object()

obj <- reactiveValues(
   dds = oobj$dds,
   rld = oobj$rld,
   res = oobj$res,
   all_dds = oobj$all_dds,
   all_rld = oobj$all_rld,
   dds_mapping = oobj$dds_mapping
)

cdata <- lapply(oobj$rld, function(x) colData(x))

coldata <- reactiveValues( all=cdata, curr=cdata )

plot_args <- reactive({
  list(
    fdr.thres=0.1,
    fc.thres=0,
    upset_data=list(genes=NULL, labels=NULL)
  )
})

gene_scratchpad <- reactive({ c('gene1', 'gene2') })

config <- reactiveVal(get_config())

shinyApp(
  ui = fluidPage(
         sidebarPanel(heatmapUI('p', 'sidebar')),
         mainPanel(heatmapUI('p', 'sidebar'))
       ),
  server = function(input, output, session){
             heatmapServer('p', obj, coldata,
                           plot_args, gene_scratchpad, config)
           }
)
}