####

# Spatial Interactive Plot (VoltRon) ####

####

####

## Background Shiny App ####

####

#' vrSpatialPlotInteractive

#'

#' @inheritParams shiny::runApp

#' @param plot_g the ggplot plot

#' @param shiny.options a list of shiny options (launch.browser, host, port etc.) passed \code{options} arguement of \link{shinyApp}. For more information, see \link{runApp}

#'

#' @importFrom shinyjs useShinyjs

#' 

#' @noRd

vrSpatialPlotInteractive <- function(plot_g = NULL, 

                                     shiny.options = list()){

  # js for Shiny

  shinyjs::useShinyjs()

  # UI

  ui <- mod_app_ui("app")

  # Server

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

    mod_app_server("app", plot_g = plot_g)

    session$onSessionEnded(function() {

      stopApp()

    })

  }

  # get shiny options

  shiny.options = configure_shiny_options(shiny.options)

  # Start Shiny Application

  shiny::runApp(

    shiny::shinyApp(ui, server, options = list(host = shiny.options[["host"]], port = shiny.options[["port"]], launch.browser = shiny.options[["launch.browser"]]),

                    onStart = function() {

                      onStop(function() {

                      })

                    })

  )

}

#' App UI

#'

#' @param id id of the module

#'

#' @import shiny

#'

#' @noRd

mod_app_ui <- function(id) {

  ns <- NS(id)

  plotOutput(ns("image_plot"),

             height = "1000px",

             dblclick = ns("plot_dblclick"),

             brush = brushOpts(

               id = ns("plot_brush"), fill = "green",

               resetOnNew = TRUE

             ))

}

#' App Server

#'

#' @param id id of the module

#' @param plot_g the ggplot plot

#'

#' @import ggplot2

#'

#' @noRd

mod_app_server <- function(id, plot_g = NULL) {

  moduleServer(id, function(input, output, session) {

    ranges <- reactiveValues(x = plot_g$coordinates$limits$x, y = plot_g$coordinates$limits$y)

    observeEvent(input$plot_dblclick, {

      brush <- input$plot_brush

      if (!is.null(brush)) {

        ranges$x <- c(brush$xmin, brush$xmax)

        ranges$y <- c(brush$ymin, brush$ymax)

      } else {

        ranges$x <- plot_g$coordinates$limits$x

        ranges$y <- plot_g$coordinates$limits$y

      }

    })

    # image output

    output$image_plot <- renderPlot({

      plot_g +

        ggplot2::coord_equal(xlim = ranges$x, ylim = ranges$y, ratio = 1)

    })

  })

}

#' configure_shiny_options

#'

#' @param shiny.options a list of shiny options (launch.browser, host, port etc.) passed \code{options} arguement of \link{shinyApp}. For more information, see \link{runApp}

#'

#' @noRd

configure_shiny_options <- function(shiny.options){

  # check package

  if (!requireNamespace('rstudioapi'))

    stop("Please install rstudioapi package to use RStudio for interactive visualization")

  # launch.browser

  if("launch.browser" %in% names(shiny.options)){

    launch.browser <- shiny.options[["launch.browser"]]

  } else {

    launch.browser <- "RStudio"

  }

  if(!is.function(launch.browser)){

    if(launch.browser == "RStudio"){

      launch.browser <- rstudioapi::viewer

    } 

  }

  # host and port

  # if "port" is entered, parse "host" (or use default) but ignore "launch.browser"

  if("host" %in% names(shiny.options)){

    host <- shiny.options[["host"]]

  } else {

    host <- getOption("shiny.host", "0.0.0.0")

  }

  if("port" %in% names(shiny.options)){

    port <- shiny.options[["port"]]

    launch.browser <- TRUE

  } else {

    port <- getOption("shiny.port")

  }

  return(list(host = host, port = port, launch.browser = launch.browser))

}

####

# Spatial Interactive Plot (Vitessce) ####

####

#' vrSpatialPlotInteractive

#'

#' Interactive Plotting identification of spatially resolved cells, spots, and ROI on associated images from multiple assays in a VoltRon object.

#'

#' @param zarr.file The zarr file of a VoltRon object

#' @param group.by a grouping label for the spatial entities

#' @param reduction The name of the reduction to visualize an embedding alongside with the spatial plot.

#' @param shiny.options a list of shiny options (host, port etc.) passed \code{options} argument of \link{wc$widget}.

#' 

#' @noRd

vrSpatialPlotVitessce <- function(zarr.file, group.by = "Sample", reduction = NULL, shiny.options = NULL) {

  # check package

  if (!requireNamespace('vitessceR'))

    stop("Please install vitessceR package for using interactive visualization!: devtools::install_github('vitessce/vitessceR')")

  # check file

  if(!dir.exists(zarr.file))

    stop(zarr.file, " is not found at the specified location!")

  # get embedding

  if(is.null(reduction)){

    obs_embedding_paths <- c("obsm/spatial")

  } else {

    obs_embedding_paths <- c(paste0("obsm/", reduction), "obsm/spatial")

  }

  # initiate vitessceR

  vc <- vitessceR::VitessceConfig$new(schema_version = "1.0.15", name = "MBrain")

  dataset <- vc$add_dataset("My dataset")

  # add ome tiff if exists

  ometiff.file <- gsub("zarr[/]?$", "ome.tiff", zarr.file)

  if(file.exists(ometiff.file)){

    w_img <- vitessceR::MultiImageWrapper$new(

      image_wrappers = list(

        vitessceR::OmeTiffWrapper$new(name="Test1", img_path=ometiff.file)

      )

    )

    dataset <- dataset$add_object(w_img)

  } 

  # add anndata

  w_data <- vitessceR::AnnDataWrapper$new(

    adata_path=zarr.file,

    obs_set_paths = c(paste0("obs/", group.by)),

    obs_set_names = c(group.by),

    obs_locations_path = "obsm/spatial",

    obs_segmentations_path = "obsm/segmentation",

    obs_embedding_paths = obs_embedding_paths

  )

  dataset <- dataset$add_object(w_data)

  # set up vitessce pane  

  spatial <- vc$add_view(dataset, vitessceR::Component$SPATIAL)

  cell_sets <- vc$add_view(dataset, vitessceR::Component$OBS_SETS)

  spatial_segmentation_layer_value <- list(opacity = 1, radius = 0, visible = TRUE, stroked = FALSE)

  spatial_layers <- vc$add_view(dataset, vitessceR::Component$LAYER_CONTROLLER)

  if(is.null(reduction)){

    vc$layout(

      vitessceR::hconcat(spatial, 

                         vitessceR::hconcat(cell_sets, spatial_layers))

    )

  } else {

    umap <- vc$add_view(dataset, vitessceR::Component$SCATTERPLOT, mapping = reduction)

    vc$layout(

      vitessceR::hconcat(spatial, 

                         vitessceR::vconcat(umap, 

                                            vitessceR::hconcat(cell_sets, spatial_layers)))

    )

  }

  if(length(shiny.options) == 0){

    vc$widget(theme = "light")

  } else {

    if (!requireNamespace('rstudioapi'))

      stop("Please install rstudioapi package!: install.packages('rstudioapi')")

    message("Listening widget from ", shiny.options[["host"]], ":", shiny.options[["port"]])

    base = rstudioapi::translateLocalUrl(paste0(shiny.options[["host"]],":",shiny.options[["port"]]), absolute=TRUE)

    vc$widget(theme = "light", base_url=base, port=shiny.options[["port"]])

  }

}