Yang-Tang / sparklinePlateMod

A shiny module for plotting microplate data as sparklines

sparklinePlateMod

A shiny module for plotting microplate data as sparklines

Introduction

This is a DT package based shiny module that can plot microplate assay data (e.g., FLIPR assay) as sparklines 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('DT')
devtools::install_github('htmlwidgets/sparkline')

Usage

1. Source the module file

source('sparklinePlateMod.R')

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

server <- function(input, output) {

  # The microplate dataframe could contain three columns:
  #   Well(chr): the well id of microplate (eg, A1, A2, B5, D12) 
  #   X(num, optional): the value to be plot on x axis of sparklines, if missing, will be generated automatically
  #   Y(num): the value to be plot on y axis of sparklines
  # The dataframe may contain other columns and will be ignored.
  
  microplate <- reactive({
    readRDS('demo_data.RDS')
  })

  # 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(slplate, id = 'YOU_MODULE_ID', data = microplate, nrow = 8, ncol = 12)

4. Add layout output ui

ui <- fluidPage(

  slplateUI('YOU_MODULE_ID')

)

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