inst/sumsamstats/server.R

In mcjmigdal/sumsamstats: Summarizing Samtools Stats Output With ATAC-seq QC in mind

library(sumsamstats)
library(dplyr)
library(ggplot2)
library(minpack.lm)
library(shiny)

exampleInput <- list.files(system.file("extdata", package = "sumsamstats"),
                           full.names = TRUE
                           )

server <- function(input, output, session) {

    data <- reactive({
        paths <- input$inputFiles$datapath
        if (is.null(paths)) {
            paths <- exampleInput
        }
        lapply(paths, readSamtoolsStats)
    })

    samples <- reactive({
        names <- input$inputFiles$name
        if (is.null(names)) {
            names <- exampleInput
        }
        gsub(".stats.txt$", "", gsub(".*/", "", names))
    })

    summaryNumbers <- reactive(do.call(rbind, lapply(1:length(data()), function(i) {
        df <- data()
        df[[i]]$SN$sample <- factor(samples()[i])
        df[[i]]$SN
    })) %>% mutate(value = as.numeric(value), description = gsub(":$", "", description)))

    insertSize <- reactive(do.call(rbind, lapply(1:length(data()), function(i) {
        df <- data()
        df[[i]]$IS$sample <- factor(samples()[i])
        df[[i]]$IS
    })) %>% mutate_if(is.character, as.numeric) %>% group_by(sample) %>% mutate(pairs_total = pairs_total / sum(pairs_total)))


    output$summaryInputSamples <- renderUI(checkboxGroupInput(inputId = "samplesSummaryNumbers", label = "Samples to show:", choices = unique(summaryNumbers()$sample),
        selected = unique(summaryNumbers()$sample)))

    output$summaryInputProperty <- renderUI(selectInput(inputId = "propertyToPlotSummaryNumbers", label = "Property to plot:",
                                                        choices = c("raw total sequences", "reads mapped and paired", "alignment rate"),
                                                        selected = "reads mapped and paired"
                                                        )
                                            )

    output$summaryNumbersPlot <- renderPlot({
        if(length(input$propertyToPlotSummaryNumbers) == 0) {
          warning("propertyToPlotSummaryNumbers input value to summaryNumbersPlot was of length 0, returning NULL plot.")
          return(NULL)
        }
        plotSummaryNumbers(data = summaryNumbers(), samples = input$samplesSummaryNumbers, what = input$propertyToPlotSummaryNumbers)
    })

    output$samplesInsertSize <- renderUI(checkboxGroupInput(inputId = "samplesInsertSize", label = "Samples to show:", choices = unique(summaryNumbers()$sample),
        selected = unique(summaryNumbers()$sample)))

    output$scaleInsertSize <- renderUI(selectInput(inputId = "scaleInsertSize", label = "Scale:", choices = c("normal", "log"), selected = "normal"))

    output$limsInsertSize <- renderUI(sliderInput(inputId = "limsInsertSize", label = "Range:", min = 0, max = 2000, value = c(0, 400)))

    output$insertSizePlot <- renderPlot({
        if (length(input$limsInsertSize) == 0 || length(input$scaleInsertSize) == 0) {
          warning("One of input values to insertSizePlot was of length 0, returning NULL plot.")
          return(NULL)
        }
        useLogScale <- ifelse(input$scaleInsertSize == "log", T, F)
        plotInsertSize(data = insertSize(), samples = input$samplesInsertSize, log = useLogScale, lims = input$limsInsertSize)

    })
}