shiny_plots.Rmd

title: "Plot Talinum RNASeq data"
output: html_document
runtime: shiny

knitr::opts_chunk$set(echo = TRUE)

# Load data

load(file = "../runs/kallisto_sleuth/run2/05_shinyPrep.RData")

# Setup plot environment 

required.packages <- c('kableExtra', ## RMarkdown, 
                      "shiny", "tidyverse", ## data loading and shaping
                       "RColorBrewer" ## plotting
                       )

for(package in required.packages)
{
  print(package)
  ## Check if package is installed. If not, install
  if(!package %in% row.names(installed.packages()))
    {install.packages(package, repos ="https://cran.uni-muenster.de/")}
  ## Load package
  library(package, character.only = T)
}

# Non-interactive test

current_selection <- sample(expression_data$target_id, 10)

plot_set <- subset(expression_data, target_id %in% current_selection)

ggplot(plot_set, aes(x = Photosynthesis.mode, y = tpm, group = Photosynthesis.mode)) + 
    stat_summary(fun = 'mean', geom = 'bar') +
    geom_point(size = 0.5) +
    facet_wrap(~ target_id , scales = "free") + 
    theme_minimal()

# Let it shine

sidebarLayout(
  
  sidebarPanel(
    
    selectizeInput(multiple = T, "target", label = "Select Gene by target id",
                   choices = available_genes, 
                   selected = sample(available_genes, size = 3),
                   options = list(delimiter = ' ',
                   create = I("function(input, callback){return {value: input, text: input};}"))
    ),
    helpText("You can copy/paste target ids from excel")
    
  ),
  
  
  mainPanel(
    
    renderPlot({
      
      
      plot_set <- subset(expression_data, target_id %in% input$target)
      
      ## Facetted by gene only
      
      ggplot(plot_set, aes(x = Photosynthesis.mode, y = tpm)) + 
        stat_summary(fun = 'mean', geom = 'bar') +
        geom_point(size = 0.5) +
        facet_wrap( ~ target_id, scales = "free") + 
        theme_minimal() + 
        theme(aspect.ratio = 1)
      
      
    }),
    
    
  )
)