layoutPlateMod

A shiny module for plotting microplate layout

Introduction

This is a highcharter package based shiny module that can display the layout of a microplate as bubble plot and return infomation of user selected wells.

Pre-request

This shiny module requires following packages. Please make sure they are installed.

install.package('dplyr')
install.package('tidyr')
install.package('highcharter')

Usage

1. Source the module file

source('layoutPlateMod.R')

2. In server function, create a shiny reactive object that contains the microplate layout data to be displayed in dataframe format:

server <- function(input, output) {

  # The microplate dataframe should contain at least four columns:
  #   Well(chr): the well id of microplate (eg, A1, A2, B5, D12) 
  #   Value(num): the value of that well to be displayed as bubble size
  #   Color_by(chr): the categorical variable that defines the color of bubble
  #   Label(chr): the label displayed on the bubble
  # The dataframe may contain other columns and will be ignored.
  
  microplate <- reactive({
    expand.grid(Row = LETTERS[1:8], Col = 1:12, stringsAsFactors = F) %>%
      unite(Well, Row, Col, sep = '') %>%
      mutate(Value = runif(n()),
             Color_by = sample(c('Group A', 'Group B', 'Group C', NA_character_), n(), T),
             Label = sample(c(1:5, NA), n(), T)) %>%
      sample_frac(0.9) %>%
      arrange(Color_by)
  })

  # other codes

}

3. Invoke module in server function and send the microplate data object to the data parameter. Set nrow and ncol to define the type of microplate:

selected <- callModule(loplate, id = 'YOU_MODULE_ID', data = microplate, nrow = 8, ncol = 12)

4. Add layout output ui

ui <- fluidPage(

  loplateUI('YOU_MODULE_ID')

)

5. Run app. Select wells by Click + Dragging or Shift + Click. The module returns a subsetted dataframe according to the selection.