Pattern plot module

Module UI & server to generate pattern plots.

Usage

patternPlotUI(id, panel, tab)

patternPlotServer(id, obj, coldata, gene_scratchpad, upset_data, config)

Arguments

id

Module id

panel

string, can be 'sidebar' or 'main'

tab

string, if 'plot' show plot settings, if 'table' show table settings; if 'both', show settings for both.

obj

reactiveValues object containing carnation object

coldata

reactiveValues object containing object metadata

gene_scratchpad

reactive containing genes selected in scratchpad

upset_data

reactive containing list with data from upset plot module

config

reactive list with config settings

Value

UI returns tagList with module UI server returns reactive with selected genes for scratchpad updates

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 )

gene_scratchpad <- reactive({ c('gene1', 'gene2') })
upset_data <- reactive({ list(genes=NULL, labels=NULL) })

config <- reactiveVal(get_config())

shinyApp(
  ui = fluidPage(
         sidebarPanel(
           patternPlotUI('p', 'sidebar', 'both'),
           conditionalPanel(condition = "input.pattern_mode == 'Plot'",
             patternPlotUI('p', 'sidebar', 'plot')
           ),
           conditionalPanel(condition = "input.pattern_mode == 'Table'",
             patternPlotUI('p', 'sidebar', 'table')
           )
         ),
         mainPanel(
           tabsetPanel(id='pattern_mode',
             tabPanel('Plot',
               patternPlotUI('p', 'plot')
             ), # tabPanel plot

             tabPanel('Cluster membership',
               patternPlotUI('p', 'table')
             ) # tabPanel cluster_membership

           ) # tabsetPanel pattern_mode
         ) # tabPanel pattern_analysis
       ),
  server = function(input, output, session){
             patternPlotServer('deg_plot', obj, coldata,
                               gene_scratchpad, upset_data, config)
           }
)
}