Generalized marker table module

Generalized marker table module

Usage

markerTableGeneralUI(id, panel, type, label = NULL)

markerTableGeneralServer(
  id,
  obj,
  type,
  genes_to_plot,
  reset_genes,
  global_args,
  args,
  reload_global,
  config
)

Arguments

id

Input id

panel

string, can be 'sidebar', 'selection' or 'main'

type

string, used to define type of table

label

string, label for table

obj

reactive list with marker tables

genes_to_plot

reactive list of genes to plot

reset_genes

reactive to trigger gene selection reset

global_args

reactive list with global settings

args

reactive list with 'max_padj', 'max_lfc'

reload_global

reactive to trigger global args reload

config

reactive list with config settings

Value

UI returns sidebar/selection/main panel UI elements for a marker table Server returns reactive expression containing marker filters and selected genes

Examples

if (FALSE) { # interactive()
marker_tbl <- data.frame(
  gene = c("GeneA", "GeneB", "GeneC", "GeneD"),
  cluster = c("A", "A", "B", "B"),
  avg_log2FC = c(1.2, 0.7, 1.1, 0.8),
  pct.1 = c(0.9, 0.8, 0.85, 0.75),
  pct.2 = c(0.2, 0.3, 0.25, 0.35),
  p_val_adj = c(0.001, 0.02, 0.005, 0.03)
)

config <- get_config()

ui <- shiny::fluidPage(
  shinyjs::useShinyjs(),
  shiny::sidebarLayout(
    shiny::sidebarPanel(
      markerTableGeneralUI(
        "allmarkers",
        panel = "sidebar",
        type = "allmarkers",
        label = "Cluster Markers"
      ),
      markerTableGeneralUI(
        "allmarkers",
        panel = "selection",
        type = "allmarkers",
        label = "Cluster Markers"
      )
    ),
    shiny::mainPanel(
      shiny::tabsetPanel(
        markerTableGeneralUI(
          "allmarkers",
          panel = "main",
          type = "allmarkers",
          label = "Cluster Markers"
        )
      ),
      shiny::verbatimTextOutput("selected")
    )
  )
)

server <- function(input, output, session) {
  selected <- markerTableGeneralServer(
    "allmarkers",
    obj = shiny::reactive({ list(markers = marker_tbl) }),
    type = "allmarkers",
    genes_to_plot = shiny::reactive({ character() }),
    reset_genes = shiny::reactive({ NULL }),
    global_args = shiny::reactive({ list() }),
    args = shiny::reactive({ list(max_padj = 0.1, min_lfc = 0) }),
    reload_global = shiny::reactiveVal(0),
    config = shiny::reactive({ config })
  )

  output$selected <- shiny::renderPrint({
    selected()
  })
}

shiny::shinyApp(ui, server)
}