ideogRam Shiny Example

Here is an example of ideogRam in Shiny.

library(shiny)
library(ideogRam)

server <- function(input, output) {
  output$ideo_01 <- renderIdeogRam({
    chromosome <- input$chromosome
    organism <- input$organism
    orientation <- input$orientation
    if (orientation == "default") {
      orientation <- NULL
    }

    barWidth <- as.numeric(input$barWidth)
    chrHeight <- as.numeric(input$chrHeight)
    chrMargin <- as.numeric(input$chrMargin)
    chrWidth <- as.numeric(input$chrWidth)

    ploidy <- input$ploidy
    rows <- input$rows
    sex <- input$sex

    rotatable <- as.logical(input$rotatable)
    showBandLabels <- as.logical(input$showBandLabels)
    showChromosomeLabels <- as.logical(input$showChromosomeLabels)
    showAnnotTooltip <- as.logical(input$showAnnotTooltip)
    showFullyBanded <- as.logical(input$showFullyBanded)
    showNonNuclearChromosomes <- as.logical(input$showNonNuclearChromosomes)

    ideogRam(
      organism = organism, chromosome = chromosome, orientation = orientation,
      barWidth = barWidth, chrHeight = chrHeight, chrMargin = chrMargin, chrWidth = chrWidth,
      ploidy = ploidy, rows = rows, sex = sex,
      rotatable = rotatable,
      showBandLabels = showBandLabels,
      showChromosomeLabels = showChromosomeLabels,
      showAnnotTooltip = showAnnotTooltip,
      showFullyBanded = showFullyBanded,
      showNonNuclearChromosomes = showNonNuclearChromosomes
    )
  })
}

ui <- shinyUI(fluidPage(
  titlePanel("Hello IdeogRam!"),
  sidebarPanel(
    width = 4,
    textInput("organism",
      label = "Organism", value = "human",
      placeholder = "Organism's name or organism's NCBI Taxonomy ID"
    ),
    textInput("chromosome",
      label = "Chromosome", value = "",
      placeholder = "Default showing all chromosomes"
    ),
    selectInput("orientation",
      label = "Orientation",
      choices = c("default", "horizontal", "vertical")
    ),
    numericInput("barWidth", label = "barWidth", value = 3, min = 1, max = 10),
    numericInput("chrHeight", label = "chrHeight", value = 400, min = 10, max = 1000, step = 10),
    numericInput("chrMargin", label = "chrMargin", value = 10, min = 0, max = 100, step = 1),
    numericInput("chrWidth", label = "chrWidth", value = 10, min = 0, max = 100, step = 1),
    numericInput("ploidy", label = "Ploidy", value = 1, min = 1, max = 8, step = 1),
    numericInput("rows", label = "rows", value = 1, min = 1, max = 5, step = 1),
    selectInput("sex", label = "sex", choices = c("male", "female")),
    checkboxInput("rotatable", label = "rotatable", value = TRUE),
    checkboxInput("showBandLabels", label = "showBandLabels", value = FALSE),
    checkboxInput("showChromosomeLabels", label = "showChromosomeLabels", value = TRUE),
    checkboxInput("showAnnotTooltip", label = "showAnnotTooltip", value = TRUE),
    checkboxInput("showFullyBanded", label = "showFullyBanded", value = TRUE),
    checkboxInput("showNonNuclearChromosomes",
      label = "showNonNuclearChromosomes",
      value = FALSE
    )
  ),
  mainPanel(
    ideogRamOutput("ideo_01")
  )
))

shinyApp(ui = ui, server = server)