loxcodeR: Loxcode Tools

library(shiny)
library(plotly)
library(DT)
library(loxcoder)
library(shinydashboard)
library(rlist)
library(shinyFiles)
library(shinyalert)
library(knitr)
library(rmarkdown)
library(yaml)
library(gridExtra)
library(testit)
library(shinyjs)

### INITIALIZE
load_origin_distmaps('/wehisan/general/user_managed/grpu_naik.s_2/TW/maps/origin/')
load_pair_distmaps('/wehisan/general/user_managed/grpu_naik.s_2/TW/maps/origin/')
#NN167_small = readRDS(file = "Loxcode_experiments/NN167_small.rds")
#NN156_small = readRDS(file = "Loxcode_experiments/NN156_small.rds")
#NN156 = readRDS(file = "Loxcode_experiments/NN156.rds")
#NN167 = readRDS(file = "Loxcode_experiments/NN167.rds")
#col = readRDS(file = "Loxcode_experiments/col.rds")

# lox <- as(NN167_small,"loxcode_experiment")
# attr(lox,"alias")=list()
# attr(lox,"order")=list()
# lox=fill_alias(lox);
#lox <- col
exp = list(lox)
d <- summary_table(lox, "all_samples")


### CONSTANTS
chart_choices = c("Statistics Plots", "Heatmap", "Saturation Plot", "Pair Comparison Plot")

header <- dashboardHeader(
  title = "LoxCodeR",
  dropdownMenuOutput("curr_lox")
)

sidebar <- dashboardSidebar(
  sidebarMenu(
    menuItem("Import", tabName="import", icon=icon("upload")),
    menuItem(
      "Create", tabName="create", icon=icon("folder-plus"),
      menuSubItem("Create Code Sets", tabName="codeset-create"),
      menuSubItem("Create Sample Sets", tabName="sample-create"),
      menuSubItem("Filter Codes", tabName="codes-filter")
    ),
    menuItem(
      "Plots", tabName="plots", icon=icon("chart-bar"),
      menuSubItem("Statistics Plots", tabName="stats-plot"),
      menuSubItem("Heat Map", tabName="heatmap-plot"),
      menuSubItem("Saturation Plot", "saturation-plot"),
      menuSubItem("Pair Comparison Plot", "pair-plot")
    ),
    menuItem("Report", tabName="report", icon=icon("file-alt")),
    menuItem("Log", tabName="log", icon=icon("history"))
  )
)

body <- dashboardBody(
  tabItems(
    tabItem(
      tabName = "import",
      box(
        width = 6,
        title = "Method 1: Upload a loxcode experiment object",
        status = NULL,
        color = NULL,
        solidHeader = TRUE,
        collapsible = TRUE,
        fileInput("rds_file", "Choose an rds file:", multiple=TRUE, accept=c("rds")),
        actionButton("submit_rds", "Upload")
      ),
      box(
        width = 6,
        title = "Method 2: Upload samplesheet and fastq directory",
        status = NULL,
        color = NULL,
        solidHeader = TRUE,
        collapsible = TRUE,
        textInput("name_exp", "Name of the loxcode experiment:", placeholder="Experiment Name"),
        fileInput("samplesheet", "Choose an xlsx file of samples", multiple=FALSE, accept=c("xlsx")),
        textInput("dir_input", "Choose a fastq directory"),
        actionButton("submit_fastq", "Upload")
      ),
      box(
        width = 12,
        title = "Loxcode Experiments",
        status = "danger",
        colour = NULL,
        solidHeader = FALSE,
        collapsible = FALSE,
        dataTableOutput("experiments_table"),
        actionButton("select_exp", "Select"),
        actionButton("merge_exp", "Merge selected"),
        actionButton("del_exp", "Delete"),
        downloadButton("save_exp", "Download Current")
      ),
      box(
        width = 12,
        title = "Sample Sheet",
        status = "danger",
        collapsible = TRUE,
        collapsed = TRUE,
        dataTableOutput("samplesheet")
      )
    ),

    tabItem(
      tabName = "codeset-create",
      fluidRow(
        box(
          title = "View a code set",
          status = NULL,
          color = NULL,
          solidHeader = TRUE,
          collapsible = TRUE,
          selectInput("view_codeset", label="Choose code set:", choices=names(lox@code_sets)),
          actionButton("delete_codeset", "Delete Code Set")
        ),
        box(
          title = "Edit code sets",
          status = NULL,
          color = "red",
          solidHeader = TRUE,
          collapsible = TRUE,
          textInput("name_codeset", label="Name of new codeset:", placeholder="Code Set Name"),
          fluidRow(
            column(4, actionButton("create_codeset", "Create from Selection")),
            column(4, actionButton("create_all_codeset", "Create from All")),
            column(4, actionButton("rename_codeset", "Rename Current"))
          )
        ),
        box(
          width = 12,
          title = "Code Set Table",
          status = "danger",
          solidHeader = FALSE,
          wellPanel(dataTableOutput("codeset_table")),
          verbatimTextOutput("selected_codes")
        )
      )
    ),

    tabItem(
      tabName = "sample-create",
      fluidRow(
        box(
          width = 6,
          title = "View a sample set",
          status = NULL,
          color = NULL,
          solidHeader = TRUE,
          collapsible = TRUE,
          selectInput("view_sample", label="Choose sample set:", choices=names(lox@count_matrixes)),
          actionButton("delete_sample", "Delete Sample Set")
        ),
        box(
          width = 6,
          title = "Edit sample sets",
          status = NULL,
          color = "red",
          solidHeader = TRUE,
          collapsible = TRUE,
          textInput("name_sample", label="Name of new sample set:", placeholder="Sample Set Name"),
          fluidRow(
            column(4, actionButton("create_sample", "Create from Selection")),
            column(4, actionButton("create_all_sample", "Create from All")),
            column(4, actionButton("rename_sample", "Rename Current"))
          )
        ),
        box(
          width = 12,
          title = "Sample Set Table",
          status = "danger",
          solidHeader = FALSE,
          wellPanel(dataTableOutput("sample_table")),
          verbatimTextOutput("selected_samples"),
          ),
        box(
          width = 6,
          title = "Generate aliases",
          status = NULL,
          solidHeader = TRUE,
          collapsible = TRUE,
          collapsed = TRUE,
          checkboxGroupInput("alias_parameters", "Choose alias parameters:", choices=c("")),
          actionButton("generate_alias", "Generate")
        ),
        box(
          width = 6,
          title = "Collapse samples",
          status = NULL,
          solidHeader = TRUE,
          collapsible = TRUE,
          collapsed = TRUE,
          textInput("collapse_name", label="Name of new sample set:", placeholder="Sample Set Name"),
          tags$strong("Collapse type: "),
          fluidRow(
            column(3, checkboxInput("collapse_union", "Union")),
            column(3, checkboxInput("collapse_average", "Average"))
          ),
          checkboxGroupInput("collapse_parameters", "Choose parameters to collapse:", choices=c("")),
          actionButton("collapse_samples", "Collapse"),
          actionButton("collapse_selection", "Collapse selected")
        )
      )
    ),

    tabItem(
      tabName = "codes-filter",
      box(
        width = 6,
        title = "View codes",
        status = NULL,
        color = NULL,
        solidHeader = TRUE,
        collapsible = TRUE,
        selectInput("independent_samples", label="Sample Set", choices=names(lox@count_matrixes)),
        selectInput("filter_codeset", label="Code Set", choices=c()),
      ),
      box(
        width = 6,
        title = "Filter parameters",
        status = NULL,
        color = NULL,
        solidHeader = TRUE,
        collapsible = TRUE,
        column(6, sliderInput("filter_reps", label="Maximum allowed code repetitions", min=1, max=10, value=1)),
        column(6, sliderInput("filter_tolerance", label="Tolerance Level (%)", min=0.1, max=100, value=5, step=0.1)),
        textInput("filter_code_name", label="Name of new filtered code set:", placeholder="Code Set Name"),
        actionButton("create_filtered", "Create Filtered Code Set")
      ),
      box(
        width = 6,
        status = "danger",
        title = "Unfiltered codes",
        collapsible = TRUE,
        collapsed = TRUE,
        plotOutput("unfiltered_codes"),
      ),
      box(
        width = 6,
        status = "danger",
        title = "Filtered codes",
        collapsible = TRUE,
        collapsed = TRUE,
        plotOutput("filtered_codes"),
      ),
    ),

    tabItem(
      tabName = "stats-plot",
      fluidRow(
        box(
          title = "View a sample set",
          width = 4,
          status = NULL,
          color = NULL,
          solidHeader = TRUE,
          collapsible = TRUE,
          selectInput("matrix_stats", "Sample:", choices = names(lox@count_matrixes))
        ),
        box(
          title = "View a code set",
          width = 4,
          status = NULL,
          color = NULL,
          solidHeader = TRUE,
          collapsible = TRUE,
          selectInput("codeset_stats", "Codes:", choices = names(lox@code_sets))
        ),
        box(
          title = "Configure the plot",
          width = 4,
          status = NULL,
          color = NULL,
          solidHeader = TRUE,
          collapsible = TRUE,
          selectInput("labels_stats", "Plot Labels:", choices = c("sample", "alias"), selected = "alias")
        ),
        box(
          width = 12,
          title = "Statistics Plots",
          status = "danger",
          collapsible = TRUE,
          collapsed = TRUE,
          tabsetPanel(
            type = "tabs",
            tabPanel(
              "Size",
              plotlyOutput("size_plot"),
              checkboxInput("fill_size", "Fill"),
              actionButton("includeSize", "Add to report")),
            tabPanel(
              "Complexity",
              plotlyOutput("complexity_plot"),
              checkboxInput("fill_complexity", "Fill"),
              actionButton("includeComplexity", "Add to report")),
            tabPanel("Ratio", plotlyOutput("ratio_plot"), actionButton("includeRatio", "Add to report")),
            tabPanel("Both", plotlyOutput("both_plot"), actionButton("includeBoth", "Add to report"))
          )
        ),
        box(
          width = 6,
          title = "Sample Size Plot",
          status = "danger",
          collapsible = TRUE,
          collapsed = TRUE,
          conditionalPanel(
            condition = "input.labels_stats=='sample'",
            selectInput("size_sample", "", choices=c()),
          ),
          conditionalPanel(
            condition = "input.labels_stats=='alias'",
            selectInput("size_alias", "", choices=c()),
          ),
          plotlyOutput("sample_size_plot"),
          actionButton("includeSampleSize", "Add to report")
        ),
        box(
          width = 6,
          title = "Sample Complexity Plot",
          status = "danger",
          collapsible = TRUE,
          collapsed = TRUE,
          conditionalPanel(
            condition = "input.labels_stats=='sample'",
            selectInput("complexity_sample", "", choices=c()),
          ),
          conditionalPanel(
            condition = "input.labels_stats=='alias'",
            selectInput("complexity_alias", "", choices=c()),
          ),
          plotlyOutput("sample_complexity_plot"),
          actionButton("includeSampleComplexity", "Add to report")
        )
      )
    ),

    tabItem(
      tabName = "heatmap-plot",
      box(
        width = 6,
        title = "View a sample set",
        status = NULL,
        color = NULL,
        solidHeader = TRUE,
        collapsible = TRUE,
        selectInput("matrix_heat", "Sample:", choices = names(lox@count_matrixes))
      ),
      box(
        width = 6,
        title = "View a code set",
        status = NULL,
        color = NULL,
        solidHeader = TRUE,
        collapsible = TRUE,
        selectInput("codeset_heat", "Codes:", choices = names(lox@code_sets))
      ),
      box(
        width = 6,
        title = "Sample Comparison Pie",
        status = "danger",
        color = NULL,
        collapsible = TRUE,
        collapsed = TRUE,
        plotOutput("sample_comparison_pie"),
        textInput("scale_pie", "Scale factor:", value=1)
      ),
      box(
        width = 6,
        title = "Configure the heatmap plot",
        status = "danger",
        color = NULL,
        collapsible = TRUE,
        collapsed = TRUE,
        selectInput("type_heat", "Plot Types:", choices = c("ggplot", "plotly")),
        selectInput("labels_heat", "Plot Labels:", choices=c("sample", "alias"), selected = "alias"),
        selectInput("clustering", "Clustering", choices=c("none", "row", "col", "both")),
        selectInput("agglomeration", "Agglomeration", choices=c("ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median","centroid","binary"),selected="complete"),
        sliderInput("min_reads", label="Minimum # reads", min=1, max=100, value=1),
        sliderInput("max_repeats", label="Maximum # repeats", min=1, max=100, value=100),
        sliderInput("min_repeats", label="Minimum # repeats", min=1, max=100, value=1)
      ),
      box(
        width = 12,
        title = "Heat Map",
        status = "danger",
        color = NULL,
        collapsible = TRUE,
        collapsed = TRUE,
        conditionalPanel(
          condition = "input.type_heat=='ggplot'",
          plotOutput("heatmap_ggplot")
        ),
        conditionalPanel(
          condition = "input.type_heat=='plotly'",
          plotlyOutput("heatmap_plotly")
        ),
        actionButton("includeHeatmap", "Add to report")
      ),
      box(
        width = 12,
        title = "Bubble Map",
        status = "danger",
        color = NULL,
        collapsible = TRUE,
        collapsed = TRUE,
        conditionalPanel(
          condition = "input.type_heat=='ggplot'",
          plotOutput("bubble_ggplot")
        ),
        conditionalPanel(
          condition = "input.type_heat=='plotly'",
          plotlyOutput("bubble_plotly")
        ),
        actionButton("includeBubble", "Add to report")
        ),
    ),

    tabItem(
      tabName = "saturation-plot",
      box(
        width = 6,
        title = "View a sample set",
        status = NULL,
        color = NULL,
        solidHeader = TRUE,
        collapsible = TRUE,
        selectInput("sampleset_sat", "Sample sets:", choices = names(lox@count_matrixes)),
        selectInput("name_sat", "Plot labels", choices = c("sample", "alias"), selected = "alias")
      ),
      box(
        width = 6,
        title = "View plot",
        status = NULL,
        color = NULL,
        solidHeader = TRUE,
        collapsible = TRUE,
        conditionalPanel(
          condition = "input.name_sat=='sample'",
          selectInput("sample_sat", "Samples:", choices = names(lox@samples))
        ),
        conditionalPanel(
          condition = "input.name_sat=='alias'",
          selectInput("alias_sat", "Samples:", choices = lox@alias[["all_samples"]]$alias)
        ),
        selectInput("codeset_sat", "Codes:", choices = names(lox@code_sets)),
        actionButton("add_sat", "Add new"),
        actionButton("remove_sat", "Remove"),
        actionButton("clear_sat", "Clear")
      ),
      box(
        width = 12,
        title = "Saturation Plot",
        status = "danger",
        collapsible = TRUE,
        collapsed = TRUE,
        plotlyOutput("saturation"),
        actionButton("includeSaturation", "Add to report")
      )
    ),

    tabItem(
      tabName = "pair-plot",
      box(
        width = 6,
        title = "Choose your samples",
        status = NULL,
        color = NULL,
        solidHeader = TRUE,
        collapsible = TRUE,
        selectInput("sampleset_pair", "Sample sets:", choices = names(lox@alias)),
        selectInput("codeset_pair", "Code Sets:", choices = names(lox@code_sets)),
        selectInput("name_pair", "Plot labels", choices = c("sample", "alias"), selected = "alias"),
        conditionalPanel(
          condition = "input.name_pair=='sample'",
          selectInput("sample1_pair", "Samples:", choices = c()),
          selectInput("sample2_pair", "Samples:", choices = c())
        ),
        conditionalPanel(
          condition = "input.name_pair=='alias'",
          selectInput("alias1_pair", "Samples:", choices = c()),
          selectInput("alias2_pair", "Samples:", choices = c())
        ),
        actionButton("add_pair", "Add new plot"),
        actionButton("remove_pair", "Remove plot"),
        actionButton("clear_pair", "Clear plots"),
      ),
      box(
        width = 6,
        title = "Configure the plot",
        status = NULL,
        color = NULL,
        solidHeader = TRUE,
        collapsible = TRUE,
        selectInput("type_pair", "Plot type", choices = c("ggplot", "plotly")),
        selectInput("colour_pair", "Colour by:", choices = c("size", "dist_orig", "firstread")),
        sliderInput("complexity_slider_pair", "Filter Distance Origin Range:", min = 0, max = 0, value = c(0,0)),
        sliderInput("size_slider_pair", "Filter Size Range:", min = 0, max = 0, value = c(0,0)),
        sliderInput("firstread_slider_pair", "Filter Firstreads Range", min = 0, max = 0, value = c(0,0))
      ),
      box(
        width = 12,
        title = "Pair Comparison Plot",
        status = "danger",
        collapsible = TRUE,
        collapsed = TRUE,
        conditionalPanel(
          condition = "input.type_pair=='ggplot'",
          plotOutput("pair_ggplot"),
        ),
        conditionalPanel(
          condition = "input.type_pair=='plotly'",
          plotlyOutput("pair_plotly"),
        ),
        actionButton("includePair", "Add to report")
      )
    ),
    tabItem(
      tabName = "report",
      box(
        width = 12,
        title = "Generate report",
        solidHeader = TRUE,
        radioButtons("format", "Document format", c("PDF", "HTML", "Word"), inline = TRUE),
        downloadButton("downloadReport")
      ),
      box(
        width = 12,
        status = "danger",
        title = "Report Components",
        dataTableOutput("components_table"),
        actionButton("remove_component", "Remove")
      )
    ),
    tabItem(
      tabName = "log",
      box(
        width = 12,
        title = "Actions",
        solidHeader = TRUE,
        actionButton("restart", "Restart", icon=icon("refresh")),
        bookmarkButton(),
        downloadButton("downloadLog"),
      ),
      box(
        width = 12,
        status = "danger",
        title = "Activity Log",
        collapsible = TRUE,
        collapsed = TRUE,
        dataTableOutput("log_table")
      )
    )
  )
)

# Define the js method that resets the page
jsResetCode <- "shinyjs.reset = function() {history.go(0)}"
enableBookmarking(store = "server")

ui <- function(request) {
  fluidPage(
    useShinyalert(),
    useShinyjs(),
    extendShinyjs(text=jsResetCode, functions=c("reset")),
    dashboardPage(header, sidebar, body, skin = "red")
  )
}