R/mod_genotypic1.R

In Viinky-Kevs/microsoftAI: GUI for phenotypic and genotypic analysis

#' genotypic1 UI Function
#'
#' @description A shiny Module.
#'
#' @param id,input,output,session Internal parameters for {shiny}.
#'
#' @noRd 
#'
#' @importFrom shiny NS tagList 
mod_genotypic1_ui <- function(id){
  ns <- NS(id)
  tagList(
    shiny::sidebarLayout(
      shiny::sidebarPanel(tags$h3("Distance Matrix"),
                          tags$br(),
                          tags$p("Genetic distances measure how genetically 
                                 similar are individuals or populations and 
                                 are based on a specific evolutionary model. 
                                 Genetic distances can be seen as summary 
                                 statistics because they take the whole data
                                 set (for example, data from SNP loci) and 
                                 summarize the genetic differentiation between 
                                 samples (individuals or populations) in a 
                                 value. One of the most used genetic distances 
                                 is Nei's genetic distance which measures 
                                 the genetic distance among populations on 
                                 the basis of their genetic identity, namely 
                                 the proportion of alleles that are shared 
                                 between populations. For our data set, we 
                                 have defined gene pools as populations in the 
                                 genind object called LimaBeanData2. 
                                 To calculate Nei's genetic distances among 
                                 populations we need to add the strata to 
                                 the genind object (in this case on the basis 
                                 of the gene pool) to define the populations. 
                                 Finally, we will build with this distance 
                                 matrix a UPGMA tree and a neighbor-joining (
                                 NJ) topology, applying 1000 bootstrap permutations 
                                 to get statistical support of the groups in the topologies."),
                          tags$br(),
                          shiny::fileInput(ns("filevcf"), "Choose a VCF file",
                                           multiple = F,
                                           accept = ".vcf",
                                           buttonLabel = "Uploading..."),
                          shiny::fileInput(ns("filetxt"), "Choose a TXT file",
                                           multiple = F,
                                           accept = ".txt",
                                           buttonLabel = "Uploading...")
      ),
      mainPanel(
                tags$br(),
                tags$h4("UPGMA topology"),
                shiny::plotOutput(ns("distance_matrix1"), height = "500px",
                                  dblclick = "double_click",
                                  brush = brushOpts(
                                    id = "brush_plot",
                                    resetOnNew = TRUE
                                  )),
                tags$h4("NJ topology"),
                plotOutput(ns("distance_matrix2"), height = "500px",
                           dblclick = "double_click2",
                           brush = brushOpts(
                             id = "brush_plot",
                             resetOnNew = TRUE
                           ))
                
      )
    )
  )
}
    
#' genotypic1 Server Functions
#' @import plotly
#' @import adegenet
#' @import randomForest
#' @import ggplot2
#' @import hierfstat
#' @import ape
#' @import poppr
#' @import pegas
#' @import vcfR
#' @import RColorBrewer
#' @import readr
#' @import tidyverse
#' @import mice
#' @import imputeTS
#' @import knitr
#' @import rgl
#' @import caTools
#' @import randomForestExplainer
#' @import dplyr
#' @import ranger
#' @import vegan
#' @import pvclust
#' @import ape
#' @import nnet
#' @import NeuralNetTools
#' @import tidyr
#' @import openxlsx
#' @import cluster
#' @import ggdendro
#' @import factoextra
#' @import foreach
#' @import gridExtra
#' @import caret
#' @import NbClust
#' @import dendextend
#' @import pals
#' @import expss
#' @import e1071
#' @import ROCR
#' @import pROC
#' @import aricode
#' @import dendextend
#' @import fpc
#' @import mclust
#' @import corrplot
#' @import scales
#' @import ggpubr
#' @import grDevices
#' @noRd 
mod_genotypic1_server <- function(id){
  moduleServer( id, function(input, output, session){
    ns <- session$ns
    
    Lima <- reactive({
      tryCatch(
        {
          LimaBeanGBS = read.vcfR(input$filevcf$datapath)
        },
        error = function(e){
          stop(safeError(e))
        }
      )
      
      tryCatch(
        {
          data = read.table(input$filetxt$datapath, header = TRUE)
        },
        error = function(e){
          stop(safeError(e))
        }
      )
      
      Genepool = as.character(data$Genepool)
      LimaBeanData2 <- vcfR2genind(LimaBeanGBS, pop= Genepool, NA.char= "NA")
      
      strata(LimaBeanData2) <- data.frame(pop(LimaBeanData2)) #to add the strata of a genind object
      nameStrata(LimaBeanData2) <- ~Genepool # to assign a name to the strata of a genind object
    })
    
    output$distance_matrix1 <- renderPlot({
      
      LimaBeanData2 <- Lima()
      #Building of a UPGMA topology with bootstrap support using the function aboot of the poppr package
      set.seed(999)
      aboot(LimaBeanData2, strata = Genepool, tree= "upgma", distance="nei.dist", sample=1000, cutoff=0, showtree=TRUE,quiet=FALSE)
      
    })
    
    output$distance_matrix2 <- renderPlot({
      LimaBeanData2 <- Lima()
      
      #Building of a UPGMA topology with bootstrap support using the function aboot of the poppr package
      set.seed(999)
      #Building of a NJ topology with bootstrap support using the function aboot of the poppr package
      aboot(LimaBeanData2, strata = Genepool, tree= "nj", distance="nei.dist", sample=1000, cutoff=0, showtree=TRUE,quiet=FALSE)
    })
    
  })
}
    
## To be copied in the UI
# mod_genotypic1_ui("genotypic1_ui_1")
    
## To be copied in the server
# mod_genotypic1_server("genotypic1_ui_1")