extended the functionality

DESCRIPTION

@@ -14,4 +14,5 @@ LazyData: true
 RoxygenNote: 6.1.1
 Imports: 
     knitr,
-    flexdashboard
+    flexdashboard,
+    yaml

NAMESPACE

@@ -4,4 +4,6 @@ export("%>%")
 exportClasses(i2dashboard)
 exportMethods(add_component)
 exportMethods(add_page)
+exportMethods(assemble)
+exportMethods(remove_page)
 importFrom(magrittr,"%>%")

R/assemble.R

+setGeneric("assemble", function(object, ...) standardGeneric("assemble"))
+
+#' Method to assemble a dashboard and write it to a file
+#'
+#' @param object A \linkS4class{i2dash::i2dashboard} object.
+#' @param output_file The output filename (recommend that the suffix should be '.Rmd'). This file will be saved in the working directory.
+#' @param pages A string or vector with the names of pages, which should be assemble to a report.
+#' @param ... Additional parameters passed to the components render function.
+#'
+#' @rdname idashboard-class
+#' @export
+setMethod("assemble", "i2dashboard", function(object, output_file, pages, ...) {
+  yaml_list <- list(title = object@title,
+                    author = object@author,
+                    output = list("flexdashboard::flex_dashboard" = list(theme = object@theme)))
+  if (object@interactive){
+    yaml_list[["runtime"]] <- "shiny"
+  }
+  yaml_part <- yaml::as.yaml(yaml_list)
+  header_string <- paste0("---\n", yaml_part, "---\n")
+
+  tmp_document <- tempfile()
+  # create variable final_document
+  final_document <- file.path(object@workdir, output_file)
+  # write header to tempfile
+  cat(header_string, file = tmp_document, append = FALSE, sep='')
+  # write page to tempfile
+  for (pagename in pages){
+    name <- .create_page_name(pagename)
+    if (name %in% names(object@pages)){
+      # Create a content string from all components
+      components <- paste0(object@pages[[name]]$components, sep = "")
+      #components <- "here are the components"
+      # Create variable "title" & "menu" & "layout" for readability
+      title <- object@pages[[name]]$title
+      menu <- object@pages[[name]]$menu
+      layout <- object@pages[[name]]$layout
+      # Check menu argument
+      if (is.null(menu)){
+        menu <- ""
+      }
+      # Check layout argument
+      if (any(layout == "storyboard")){
+        layout <- ".storyboard"
+      } else {
+        if(!is.null(layout)) warning("layout argument is not known.")
+        layout <- ""
+      }
+      layout_with_menu <- sprintf('{%s data-navmenu="%s"}', layout, menu)
+      timestamp <- Sys.time()
+      full_content <- knitr::knit_expand(file = system.file("templates", "page_template.Rmd", package = "i2dash"), title = title, layout_with_menu = layout_with_menu, components = components, date = timestamp)
+      cat(full_content, file = tmp_document, append = TRUE, sep='')
+
+      #cat(object@pages[[name]]$header, file = tmp_document, append = TRUE, sep='')
+      #cat(object@pages[[name]]$components, file = tmp_document, append = TRUE, sep='')
+    } else {
+      warning(sprintf("i2dashboard object does not contain Pagename '%s'", pagename))
+    }
+  }
+  # copy tempfile to final_document
+  file.copy(from = tmp_document, to = final_document, overwrite = TRUE)
+})
\ No newline at end of file

R/components.R

@@ -9,7 +9,7 @@ setGeneric("add_component", function(object, ...) standardGeneric("add_component
 #'
 #' @rdname idashboard-class
 #' @export
-setMethod("add_component", "i2dashboard", function(object, page, component, ...) {
+setMethod("add_component", "i2dashboard", function(object, page = "default", component, ...) {
   pn <- strsplit(component, "::")[[1]]
   eval_function <- if(length(pn) == 1) {
     get(paste0("render_", pn[[1]]), envir = asNamespace("i2dash"), mode = "function")
@@ -17,7 +17,13 @@ setMethod("add_component", "i2dashboard", function(object, page, component, ...)
     get(paste0("render_", pn[[2]]), envir = asNamespace(pn[[1]]), mode = "function")
   }
 
-  component <- do.call(eval_function, args = list(...))
-  object@pages[[page]]$components <- append(object@pages[[page]]$components, component)
+  component <- do.call(eval_function, args = list(object, ...))
+
+  name <- .create_page_name(page)
+  if (name %in% names(object@pages)){
+    object@pages[[name]]$components <- append(object@pages[[name]]$components, component)
+  } else {
+    warning(sprintf("i2dashboard object does not contain Pagename %s", name))
+  }
   return(object)
 })

R/features_by_factors.R

+#' Renders a features by factor violin plot
+#'
+#' @param plot_title The title of the Component
+#' @param x A list with the x-axis values. If it is a nested list, a dropdown-field will be provided in the interactive mode.
+#' @param y A list with the y-axis values. If it is a nested list, a dropdown-field will be provided in the interactive mode.(Needs to be categorial. Horizontal violinplots are not possible.)
+#'
+#' @return A string containing markdown code for the rendered textbox
+render_features_by_factors <- function(object, plot_title, x, y) {
+
+  env_id <- .create_id()
+  # validate input, create environment variables, save environment object
+  .validate_input_ff(object, env_id, x, y)
+  timestamp <- Sys.time()
+  expanded_component <- knitr::knit_expand(file = system.file("templates", "features_by_factors_template.Rmd", package = "i2dash"), plot_title = plot_title, env_id = env_id, date = timestamp)
+  return(expanded_component)
+}
+
+.create_id <- function(n = 1) {
+  a <- do.call(paste0, replicate(5, sample(LETTERS, n, TRUE), FALSE))
+  paste0(a, sprintf("%04d", sample(9999, n, TRUE)), sample(LETTERS, n, TRUE))
+}
+
+.validate_input_ff <- function(object, env_id, x, y) {
+  env <- new.env()
+  env$x_selection <- FALSE
+  env$y_selection <- FALSE
+
+  # validate x and create environment variables
+  if(is.list(x) & length(x) == 1) {
+    if (is.factor(x[[1]])){
+      env$x <- x
+    } else {
+      stop("x should contain factors")
+    }
+
+  } else if (is.list(x) & length(x) > 1) {
+    for (i in length(x)){
+      if (is.factor(x[[i]])){
+        env$x_selection <- TRUE
+        env$x <- x
+      } else {
+        stop("x should contain only factors")
+      }
+    }
+  } else if (!is.list(x) | (is.list(x) & length(x) == 0)){
+    stop("x needs to be a named list with at least one element")
+  }
+
+  # validate y and create environment variables
+  if(is.list(y) & length(y) == 1) {
+    env$y <- y
+  } else if (is.list(y) & length(y) > 1) {
+    env$y_selection <- TRUE
+    env$y <- y
+  } else if (!is.list(y) | (is.list(y) & length(y) == 0)){
+    stop("y needs to be a named list with at least one element")
+  }
+
+  # save environment as rds-object
+  saveRDS(env, file = file.path(object@workdir, "envs", sprintf("%s.rds", env_id)))
+}
\ No newline at end of file

R/i2dashboard.R

 #' The idashboard S4 class
 #'
 #' @slot title The dashboards title
+#' @slot author The author of the dashboard
+#' @slot interactive If a shiny-based report should be created
+#' @slot theme The theme of the dashboard
 #' @slot pages A list of dashboard pages
 #'
 #' @name idashboard-class
 #' @rdname idashboard-class
 #' @export
-i2dashboard <- setClass("i2dashboard",
-                        slots = c(title = "character", pages = "list"))
+setClass("i2dashboard",
+  slots = c(
+    title = "character",
+    author = "character",
+    interactive = "logical",
+    theme = "character",
+    workdir = "character",
+    pages = "list"
+    ),
+  prototype=list(
+    theme = "yeti",
+    pages = list(default = list(title = "Default page", layout = NULL, menu = NULL, components = list()))
+    )
+  )
 
 setMethod("show", "i2dashboard", function(object) {
   cat("A flexdashboard with the title: ", object@title, "\n", sep = "")
   if(length(object@pages) > 0) {
-    cat("... containing ", length(object@pages), "pages.")
+    cat("... containing ", length(object@pages), "pages:\n")
+    for (pagename in names(object@pages)){
+      cat(sprintf(" ... the page '%s' with the title '%s' contains %i components.\n", pagename, object@pages[[pagename]]$title, length(object@pages[[pagename]]$components)))
+    }
   } else {
     cat("... containing 0 pages.")
   }
 })
+
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+### Validity.
+###
+
+# .valid.RmdReport <- function(object){
+#   msg <- NULL
+#   # Checking header
+#   if (!is.character(object@header)){
+#     msg <- c(msg, "'header' must be a character-like object")
+#   }
+#   # Checking pages
+#   if (!is.list(object@pages)){
+#     msg <- c(msg, "'pages' must be a list-like object")
+#   }
+#   if (length(msg)) { return(msg) }
+#   return(TRUE)
+# }
+#
+# setValidity("RmdReport", .valid.RmdReport)

R/multiplot.R

+#' Renders a Sequence saturation plot
+#'
+#' @param plot_title The title of the Component
+#' @param x A list with the x-axis values. If it is a nested list, a dropdown-field will be provided in the interactive mode.
+#' @param y A list with the y-axis values. If it is a nested list, a dropdown-field will be provided in the interactive mode.
+#' @param color_by A list with the color_by values. If it is a nested list, a dropdown-field will be provided in the interactive mode.
+#'
+#' @return A string containing markdown code for the rendered textbox
+render_multiplot <- function(object, plot_title, x, y, color_by) {
+
+  env_id <- .create_id()
+  # validate input, create environment variables, save environment object
+  .validate_input(object, env_id, x, y, color_by)
+  timestamp <- Sys.time()
+  expanded_component <- knitr::knit_expand(file = system.file("templates", "multiplot_template.Rmd", package = "i2dash"), plot_title = plot_title, env_id = env_id, date = timestamp)
+  return(expanded_component)
+}
+
+.create_id <- function(n = 1) {
+  a <- do.call(paste0, replicate(5, sample(LETTERS, n, TRUE), FALSE))
+  paste0(a, sprintf("%04d", sample(9999, n, TRUE)), sample(LETTERS, n, TRUE))
+}
+
+.validate_input <- function(object, env_id, x, y, color_by) {
+  env <- new.env()
+  env$x_selection <- FALSE
+  env$y_selection <- FALSE
+  env$color_selection <- FALSE
+
+  # validate x and create environment variables
+  if(is.list(x) & length(x) == 1) {
+    env$x <- x
+  } else if (is.list(x) & length(x) > 1) {
+    env$x_selection <- TRUE
+    env$x <- x
+  } else if (!is.list(x) | (is.list(x) & length(x) == 0)){
+    stop("x needs to be a named list with at least one element")
+  }
+
+  # validate y and create environment variables
+  if(is.list(y) & length(y) == 1) {
+    env$y <- y
+  } else if (is.list(y) & length(y) > 1) {
+    env$y_selection <- TRUE
+    env$y <- y
+  } else if (!is.list(y) | (is.list(y) & length(y) == 0)){
+    stop("y needs to be a named list with at least one element")
+  }
+
+  # validate color_by and create environment variables
+  if(is.list(color_by) & length(color_by) == 1) {
+    env$color_by <- color_by
+  } else if (is.list(color_by) & length(color_by) > 1) {
+    env$color_selection <- TRUE
+    env$color_by <- color_by
+  } else if (!is.list(color_by) | (is.list(color_by) & length(color_by) == 0)){
+    stop("color_by needs to be a named list with at least one element")
+  }
+  # for (i in color_by){
+  #   if (!is.factor(i)){
+  #     stop("color_by needs to be a list with factorial elements")
+  #   }
+  # }
+
+  # save environment as rds-object
+  saveRDS(env, file = file.path(object@workdir, "envs", sprintf("%s.rds", env_id)))
+}
\ No newline at end of file

R/pages.R

@@ -21,14 +21,53 @@ setGeneric("add_page", function(object, ...) standardGeneric("add_page"))
 #'
 #' @rdname idashboard-class
 #' @export
-setMethod("add_page", "i2dashboard", function(object, page, title, layout = "storyboard", menu = title, ...) {
+setMethod("add_page", "i2dashboard", function(object, page, title, layout = "storyboard", menu = NULL, ...) {
   name <- .create_page_name(page)
-  object@pages[[name]] <- list(title = title, layout = layout, menu = menu, components = list())
 
+  # Create working directory and directory for environments
+  dir.create(object@workdir, showWarnings = FALSE)
+  dir.create(file.path(object@workdir, "envs"), recursive = T, showWarnings = FALSE)
+
+  if (name %in% names(object@pages)){
+    print("A page with this 'page'-argument already exists.")
+    answer1 <- menu(c("Yes", "No"), title="Do you want to overwrite this page? If 'No' you can input another 'page'-argument or cancel.")
+    switch (answer1,
+    "1"={
+      print("The page was overwritten.")
+      object@pages[[name]] <- list(title = title, layout = layout, menu = menu, components = list())
+    },
+    "2"={
+      answer2 <- menu(c("Yes", "Cancel"), title="Do you want to provide another 'page'-argument?")
+      switch (answer2,
+        "1"={
+          new_name <- readline("Please input a new 'page'-argument: ")
+          if (is.character(new_name)){
+            new_name <- .create_page_name(new_name)
+            print("Page with new 'page'-argument created.")
+            object@pages[[new_name]] <- list(title = title, layout = layout, menu = menu, components = list())
+          }
+        },
+        "2"={
+          print("Function 'add_page' canceled")
+        }
+      )
+    }
+    )
+  } else {
+    object@pages[[name]] <- list(title = title, layout = layout, menu = menu, components = list())
+  }
   return(object)
 })
 
 setGeneric("remove_page", function(object, ...) standardGeneric("remove_page"))
+
+#' Method to remove a page to an i2dashboard object
+#'
+#' @param object A \linkS4class{i2dash::i2dashboard} object.
+#' @param page The name of the page to be removed.
+#'
+#' @rdname idashboard-class
+#' @export
 setMethod("remove_page", "i2dashboard", function(object, page) {
   name <- .create_page_name(page)
   object@pages[[name]] <- NULL

R/sequence_saturation.R

+#' Renders a Sequence saturation plot
+#'
+#' @param plot_title The title of the Component
+#' @param x A list with the x-axis values. If it is a nested list, a dropdown-field will be provided in the interactive mode.
+#' @param y A list with the y-axis values. If it is a nested list, a dropdown-field will be provided in the interactive mode.
+#' @param color_by A list with the color_by values. If it is a nested list, a dropdown-field will be provided in the interactive mode.
+#'
+#' @return A string containing markdown code for the rendered textbox
+render_sequence_saturation <- function(object, plot_title, x, y, color_by) {
+
+  env_id <- .create_id()
+  # validate input, create environment variables, save environment object
+  .validate_input(object, env_id, x, y, color_by)
+  timestamp <- Sys.time()
+  expanded_component <- knitr::knit_expand(file = system.file("templates", "sequence_saturation_template.Rmd", package = "i2dash"), plot_title = plot_title, env_id = env_id, date = timestamp)
+  return(expanded_component)
+}
+
+.create_id <- function(n = 1) {
+  a <- do.call(paste0, replicate(5, sample(LETTERS, n, TRUE), FALSE))
+  paste0(a, sprintf("%04d", sample(9999, n, TRUE)), sample(LETTERS, n, TRUE))
+}
+
+.validate_input <- function(object, env_id, x, y, color_by) {
+  env <- new.env()
+  env$x_selection <- FALSE
+  env$y_selection <- FALSE
+  env$color_selection <- FALSE
+
+  # validate x and create environment variables
+  if(is.list(x) & length(x) == 1) {
+    env$x <- x
+  } else if (is.list(x) & length(x) > 1) {
+    env$x_selection <- TRUE
+    env$x <- x
+  } else if (!is.list(x) | (is.list(x) & length(x) == 0)){
+    stop("x needs to be a named list with at least one element")
+  }
+
+  # validate y and create environment variables
+  if(is.list(y) & length(y) == 1) {
+    env$y <- y
+  } else if (is.list(y) & length(y) > 1) {
+    env$y_selection <- TRUE
+    env$y <- y
+  } else if (!is.list(y) | (is.list(y) & length(y) == 0)){
+    stop("y needs to be a named list with at least one element")
+  }
+
+  # validate color_by and create environment variables
+  if(is.list(color_by) & length(color_by) == 1) {
+    env$color_by <- color_by
+  } else if (is.list(color_by) & length(color_by) > 1) {
+    env$color_selection <- TRUE
+    env$color_by <- color_by
+  } else if (!is.list(color_by) | (is.list(color_by) & length(color_by) == 0)){
+    stop("color_by needs to be a named list with at least one element")
+  }
+  # for (i in color_by){
+  #   if (!is.factor(i)){
+  #     stop("color_by needs to be a list with factorial elements")
+  #   }
+  # }
+
+  # save environment as rds-object
+  saveRDS(env, file = file.path(object@workdir, "envs", sprintf("%s.rds", env_id)))
+}
\ No newline at end of file

R/textbox.R

-#' Renders a textbox with arbitrary content
-#'
-#' @param title The title of the textbox
-#' @param content The content of the textbox
-#'
-#' @return A string containing markdown code for the rendered textbox
-render_textbox <- function(title, content) {
-  knitr::knit_expand(file = system.file("templates", "textbox.Rmd", package = "i2dash"), title = title, content = content)
-}
\ No newline at end of file

inst/templates/features_by_factors_template.Rmd

+
+### {{plot_title}}
+
+<!-- Page created on {{ date }} -->
+```{r}
+{{ env_id }} = readRDS("envs/{{ env_id }}.rds")
+
+plotly::plotlyOutput("plot_{{ env_id }}")
+output$plot_{{ env_id }} <- plotly::renderPlotly({
+
+  if (!{{ env_id }}$x_selection){
+    x_value <- {{ env_id }}$x[[1]]
+    x_title <- names({{ env_id }}$x)
+  } else {
+    x_value <- {{ env_id }}$x[[input$select_x_{{ env_id }}]]
+    x_title <- input$select_x_{{ env_id }}
+  }
+
+  if (!{{ env_id }}$y_selection){
+    y_value <- {{ env_id }}$y[[1]]
+    y_title <- names({{ env_id }}$y)
+  } else {
+    y_value <- {{ env_id }}$y[[input$select_y_{{ env_id }}]]
+    y_title <- input$select_y_{{ env_id }}
+  }
+
+  p <- plotly::plot_ly(data.frame(x_value, y_value),
+               x = x_value,
+               y = y_value,
+               split = x_value,
+               type = 'violin',
+               box = list(
+                 visible = T
+                 ),
+               meanline = list(
+                 visible = T
+                 )
+               )
+p <- plotly::layout(p,
+                    xaxis = list(title = x_title),
+                    yaxis = list(title = y_title,
+                                 zeroline = F))
+
+p
+})
+```
+
+***
+
+```{r}
+# selection field for x
+if ({{ env_id }}$x_selection){
+  selectInput("select_x_{{ env_id }}", label = "Select data for x axis:",
+            choices = names({{ env_id }}$x))
+}
+
+# selection field for y
+if ({{ env_id }}$y_selection){
+  selectInput("select_y_{{ env_id }}", label = "Select data for y axis:",
+            choices = names({{ env_id }}$y))
+}
+```
+
+Plot description:
+
+Sequencing is called *saturated* when generating more sequencing output from a cDNA library does not substantially increase the number of detected features in a sample. Since the number of detected features can act as a technical confounder, and thereby drive substructure in the data, it is advisable to aim for a saturated sequencing by either adding more sequencing output or decreasing the number of samples until saturation is achieved. [@zhang_one_2018] gives advise on how to choose the optimal cell number given a fixed sequencing budget
+

inst/templates/multiplot_template.Rmd

+
+### {{plot_title}}
+
+<!-- Component created on {{ date }} -->
+```{r}
+{{ env_id }} = readRDS("envs/{{ env_id }}.rds")
+df <- data.frame({{ env_id }}$x, {{ env_id }}$y, {{ env_id }}$color_by)
+df.melted <- reshape::melt(df, id=c(names({{ env_id }}$y), names({{ env_id }}$color_by)))
+
+plotly::plotlyOutput("plot_{{ env_id }}")
+output$plot_{{ env_id }} <- plotly::renderPlotly({
+
+  if (!{{ env_id }}$y_selection){
+    index_y <- match(names({{ env_id }}$y), names(df.melted))
+  } else {
+    index_y <- match(input$select_y_{{ env_id }}, names(df.melted))
+  }
+
+  if (!{{ env_id }}$color_selection){
+    index_color <- match(names({{ env_id }}$color_by), names(df.melted))
+  } else {
+    index_color <- match(input$select_color_{{ env_id }}, names(df.melted))
+  }
+  
+  g1 <- ggplot2::ggplot(df.melted, mapping = ggplot2::aes(y = value, x = df.melted[,index_y], color = df.melted[,index_color])) +
+    ggplot2::geom_jitter() +
+    ggplot2::geom_violin(mapping = ggplot2::aes(y = value), scale = "count") +
+    ggplot2::facet_grid(. ~ variable, scales = "free_x") +
+    ggplot2::theme_bw() +
+    ggplot2::theme(panel.border = ggplot2::element_blank()) +
+    ggplot2::scale_colour_viridis_c() +
+    ggplot2::coord_flip() +
+    ggplot2::labs( y="Type", x="", color=names(df.melted)[index_color])
+
+  plotly::ggplotly(g1)
+})
+```
+
+***
+
+```{r}
+# selection field for y
+if ({{ env_id }}$y_selection){
+  selectInput("select_y_{{ env_id }}", label = "Select data for y axis:",
+            choices = names({{ env_id }}$y))
+}
+
+# selection field for color_by
+if ({{ env_id }}$color_selection){
+  selectInput("select_color_{{ env_id }}", label = "Select experimental factor for coloring:",
+            choices = names({{ env_id }}$color_by))
+}
+```
+
+Plot description:
+
+Sequencing is called *saturated* when generating more sequencing output from a cDNA library does not substantially increase the number of detected features in a sample. Since the number of detected features can act as a technical confounder, and thereby drive substructure in the data, it is advisable to aim for a saturated sequencing by either adding more sequencing output or decreasing the number of samples until saturation is achieved. [@zhang_one_2018] gives advise on how to choose the optimal cell number given a fixed sequencing budget
+

inst/templates/page_template.Rmd

+
+{{ title }} {{ layout_with_menu }}
+=========================================
+
+<!-- Page created on {{ date }} -->
+{{ components }}
\ No newline at end of file

inst/templates/sequence_saturation_template.Rmd

+
+### {{plot_title}}
+
+<!-- Component created on {{ date }} -->
+```{r}
+{{ env_id }} = readRDS("envs/{{ env_id }}.rds")
+
+plotly::plotlyOutput("plot_{{ env_id }}")
+output$plot_{{ env_id }} <- plotly::renderPlotly({
+
+  if (!{{ env_id }}$x_selection){
+    x_value <- {{ env_id }}$x[[1]]
+    x_title <- names({{ env_id }}$x)
+  } else {
+    x_value <- {{ env_id }}$x[[input$select_x_{{ env_id }}]]
+    x_title <- input$select_x_{{ env_id }}
+  }
+
+  if (!{{ env_id }}$y_selection){
+    y_value <- {{ env_id }}$y[[1]]
+    y_title <- names({{ env_id }}$y)
+  } else {
+    y_value <- {{ env_id }}$y[[input$select_y_{{ env_id }}]]
+    y_title <- input$select_y_{{ env_id }}
+  }
+
+  if (!{{ env_id }}$color_selection){
+    color_value <- {{ env_id }}$color_by[[1]]
+  } else {
+    color_value <- {{ env_id }}$color_by[[input$select_color_{{ env_id }}]]
+  }
+
+  p <- plotly::plot_ly(data.frame(x_value, y_value, color_value),
+               x = x_value,
+               y = y_value,
+               color = color_value
+  )
+  p <- plotly::layout(p,
+              xaxis = list(title = x_title),
+              yaxis = list(title = y_title))
+  p
+})
+```
+
+***
+
+```{r}
+# selection field for x
+if ({{ env_id }}$x_selection){
+  selectInput("select_x_{{ env_id }}", label = "Select data for x axis:",
+            choices = names({{ env_id }}$x))
+}
+
+# selection field for y
+if ({{ env_id }}$y_selection){
+  selectInput("select_y_{{ env_id }}", label = "Select data for y axis:",
+            choices = names({{ env_id }}$y))
+}
+
+# selection field for color_by
+if ({{ env_id }}$color_selection){
+  selectInput("select_color_{{ env_id }}", label = "Select experimental factor for coloring:",
+            choices = names({{ env_id }}$color_by))
+}
+```
+
+Plot description:
+
+Sequencing is called *saturated* when generating more sequencing output from a cDNA library does not substantially increase the number of detected features in a sample. Since the number of detected features can act as a technical confounder, and thereby drive substructure in the data, it is advisable to aim for a saturated sequencing by either adding more sequencing output or decreasing the number of samples until saturation is achieved. [@zhang_one_2018] gives advise on how to choose the optimal cell number given a fixed sequencing budget
+

inst/templates/textbox.Rmd

-### {{ title }}
+### {{ page_title }}
+
+{{ content }}  {.storyboard}
 
-{{ content }}
\ No newline at end of file

man/idashboard-class.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/components.R, R/i2dashboard.R, R/pages.R
+% Please edit documentation in R/assemble.R, R/components.R, R/i2dashboard.R,
+%   R/pages.R
 \docType{methods}
-\name{add_component,i2dashboard-method}
+\name{assemble,i2dashboard-method}
+\alias{assemble,i2dashboard-method}
 \alias{add_component,i2dashboard-method}
 \alias{idashboard-class}
-\alias{i2dashboard}
 \alias{add_page,i2dashboard-method}
-\title{Method to add a component to a page of an i2dashboard object}
+\alias{remove_page,i2dashboard-method}
+\title{Method to assemble a dashboard and write it to a file}
 \usage{
-\S4method{add_component}{i2dashboard}(object, page, component, ...)
+\S4method{assemble}{i2dashboard}(object, output_file, pages, ...)
+
+\S4method{add_component}{i2dashboard}(object, page = "default",
+  component, ...)
 
 \S4method{add_page}{i2dashboard}(object, page, title,
-  layout = "storyboard", menu = title, ...)
+  layout = "storyboard", menu = NULL, ...)
+
+\S4method{remove_page}{i2dashboard}(object, page)
 }
 \arguments{
 \item{object}{A \linkS4class{i2dash::i2dashboard} object.}
 
-\item{page}{The name of the page to add the component to.}
+\item{output_file}{The output filename (recommend that the suffix should be '.Rmd'). This file will be saved in the working directory.}
 
-\item{component}{The name of the component.}
+\item{pages}{A string or vector with the names of pages, which should be assemble to a report.}
 
 \item{...}{Additional parameters passed to the components render function.}
 
+\item{page}{The name of the page to add the component to.}
+
+\item{component}{The name of the component.}
+
 \item{title}{The title of the page to be added.}
 
 \item{layout}{The page layout (see below).}
@@ -30,20 +41,38 @@
 
 \item{object}{A \linkS4class{i2dash::i2dashboard} object.}
 
+\item{...}{Additional parameters passed to the components render function.}
+
+\item{object}{A \linkS4class{i2dash::i2dashboard} object.}
+
 \item{page}{The name of the page to be added.}
+
+\item{object}{A \linkS4class{i2dash::i2dashboard} object.}
+
+\item{page}{The name of the page to be removed.}
 }
 \description{
+Method to assemble a dashboard and write it to a file
+
 Method to add a component to a page of an i2dashboard object
 
 The idashboard S4 class
 
 Method to add a page to an i2dashboard object
+
+Method to remove a page to an i2dashboard object
 }
 \section{Slots}{
 
 \describe{
 \item{\code{title}}{The dashboards title}
 
+\item{\code{author}}{The author of the dashboard}
+
+\item{\code{interactive}}{If a shiny-based report should be created}
+
+\item{\code{theme}}{The theme of the dashboard}
+
 \item{\code{pages}}{A list of dashboard pages}
 }}
 

man/render_features_by_factors.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/features_by_factors.R
+\name{render_features_by_factors}
+\alias{render_features_by_factors}
+\title{Renders a features by factor violin plot}
+\usage{
+render_features_by_factors(object, plot_title, x, y)
+}
+\arguments{
+\item{plot_title}{The title of the Component}
+
+\item{x}{A list with the x-axis values. If it is a nested list, a dropdown-field will be provided in the interactive mode.}
+
+\item{y}{A list with the y-axis values. If it is a nested list, a dropdown-field will be provided in the interactive mode.(Needs to be categorial. Horizontal violinplots are not possible.)}
+}
+\value{
+A string containing markdown code for the rendered textbox
+}
+\description{
+Renders a features by factor violin plot
+}

man/render_multiplot.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/multiplot.R
+\name{render_multiplot}
+\alias{render_multiplot}
+\title{Renders a Sequence saturation plot}
+\usage{
+render_multiplot(object, plot_title, x, y, color_by)
+}
+\arguments{
+\item{plot_title}{The title of the Component}
+
+\item{x}{A list with the x-axis values. If it is a nested list, a dropdown-field will be provided in the interactive mode.}
+
+\item{y}{A list with the y-axis values. If it is a nested list, a dropdown-field will be provided in the interactive mode.}
+
+\item{color_by}{A list with the color_by values. If it is a nested list, a dropdown-field will be provided in the interactive mode.}
+}
+\value{
+A string containing markdown code for the rendered textbox
+}
+\description{
+Renders a Sequence saturation plot
+}

man/render_sequence_saturation.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/sequence_saturation.R
+\name{render_sequence_saturation}
+\alias{render_sequence_saturation}
+\title{Renders a Sequence saturation plot}
+\usage{
+render_sequence_saturation(object, plot_title, x, y, color_by)
+}
+\arguments{
+\item{plot_title}{The title of the Component}
+
+\item{x}{A list with the x-axis values. If it is a nested list, a dropdown-field will be provided in the interactive mode.}
+
+\item{y}{A list with the y-axis values. If it is a nested list, a dropdown-field will be provided in the interactive mode.}
+
+\item{color_by}{A list with the color_by values. If it is a nested list, a dropdown-field will be provided in the interactive mode.}
+}
+\value{
+A string containing markdown code for the rendered textbox
+}
+\description{
+Renders a Sequence saturation plot
+}

man/render_textbox.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/textbox.R
-\name{render_textbox}
-\alias{render_textbox}
-\title{Renders a textbox with arbitrary content}
-\usage{
-render_textbox(title, content)
-}
-\arguments{
-\item{title}{The title of the textbox}
-
-\item{content}{The content of the textbox}
-}
-\value{
-A string containing markdown code for the rendered textbox
-}
-\description{
-Renders a textbox with arbitrary content
-}