Gene plot module

UI & server for module to create gene plot

Usage

genePlotUI(id, panel)

genePlotServer(id, obj, coldata, plot_args, 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 list with 3 elements: 'gene.id' (all gene IDs) & 'gene_scratchpad' (genes selected in scratchpad) & 'comp_all' (selected comparison)

config

reactive list with config settings

Value

UI returns tagList with gene plot 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
)

# Set up coldata structure that the module expects
coldata <- reactiveValues(
  curr = list(
    all_samples = colData(oobj$dds$main),
    main = colData(oobj$dds$main)
  )
)

plot_args <- reactive({
  list(
    gene.to.plot = c("gene1", "gene2"),
    gene.id = rownames(oobj$dds$main),
    comp_all = "comp1"
  )
})

config <- reactiveVal(get_config())

shinyApp(
  ui = fluidPage(
         sidebarPanel(genePlotUI('p', 'sidebar')),
         mainPanel(genePlotUI('p', 'main'))
       ),
  server = function(input, output, session){
             genePlotServer('p', obj, coldata, plot_args, config)
           }
)
}