Moved datadir, added header template, bumped version

DESCRIPTION

 Package: i2dash
 Type: Package
 Title: Iterative and Interactive Dashboards in R
-Version: 0.1.0
+Version: 0.2
 Authors@R: c(
     person(given = "Arsenij", family = "Ustjanzew", email = "arsenij.ustjanzew@mpi-bn.mpg.de", role = c("aut", "cre")),
     person(given = "Jens", family = "Preussner", email = "jens.preussner@mpi-bn.mpg.de", role = c("aut"), comment = c(ORCID = "0000-0003-1927-3458")),
-    person(given = "Mario", family = "Looso", email = "mario.looso@mpi-bn.mpg.de", role = "aut"))
-Description: Iteratively create interactive flexdashboards in R.
-    Use four spaces when indenting paragraphs within the Description.
+    person(given = "Mario", family = "Looso", email = "mario.looso@mpi-bn.mpg.de", role = c("aut"), comment = c(ORCID = "0000-0003-1495-9530")))
+Description: Easily build dashboards from individual components in HTML and Shiny.
 License: MIT
 Encoding: UTF-8
 LazyData: true

R/assemble.R

-#' Method to assemble a dashboard and write it to a file
+#' Method to assemble a dashboard to a Rmd 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.
+#' @param file The output filename (recommend that the suffix should be '.Rmd'). This file will be saved in the working directory.
 #'
 #' @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<!-- This dashboard was created with the R package 'i2dash'. https://gitlab.gwdg.de/loosolab/software/i2dash -->\n")
-
+setMethod("assemble", "i2dashboard", function(object, pages = names(object@pages), file = object@file) {
   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="")
+  # Add YAML header
+  knitr::knit_expand(file = system.file("templates", "yaml_header.Rmd", package = "i2dash"),
+                     delim = c("<%", "%>"),
+                     title = object@title,
+                     author = object@author,
+                     theme = object@theme,
+                     interactive = object@interactive) %>%
+    cat(file = tmp_document, append = FALSE, sep = "\n")
 
   # Add i2dash global setup
-  cat(readLines(system.file("templates", "i2dash-global-setup.Rmd", package = "i2dash")),
-      file = tmp_document,
-      append = TRUE,
-      sep = "\n")
+  knitr::knit_expand(file = system.file("templates", "i2dash-global-setup.Rmd", package = "i2dash"), delim = c("<%", "%>"), datadir = object@datadir) %>%
+    cat(file = tmp_document, append = TRUE, sep = "\n")
 
   # write page to tempfile
   for (pagename in pages){
@@ -41,21 +28,20 @@ setMethod("assemble", "i2dashboard", function(object, output_file, pages, ...) {
     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
       sidebar <- object@pages[[name]]$sidebar
 
-      full_content <- .render_page(title = title, components = components, layout = layout,  menu = menu, sidebar = sidebar)
-      cat(full_content, file = tmp_document, append = TRUE, sep='')
+      .render_page(title = title, components = components, layout = layout,  menu = menu, sidebar = sidebar) %>%
+        cat(file = tmp_document, append = TRUE, sep='')
     } else {
       warning(sprintf("i2dashboard object does not contain a page named '%s'", pagename))
     }
   }
   # copy tempfile to final_document
-  file.copy(from = tmp_document, to = final_document, overwrite = TRUE)
+  file.copy(from = tmp_document, to = file, overwrite = TRUE)
 
   invisible(object)
 })

R/i2dashboard.R

@@ -4,6 +4,8 @@
 #' @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 data.dir
+#' @slot file
 #' @slot pages A list of dashboard pages
 #'
 #' @name idashboard-class
@@ -15,13 +17,15 @@ setClass("i2dashboard",
     author = "character",
     interactive = "logical",
     theme = "character",
-    workdir = "character",
+    datadir = "character",
+    file = "character",
     pages = "list"
     ),
   prototype=list(
+    title = "i2dashboard",
     interactive = FALSE,
     theme = "yeti",
-    workdir = getwd(),
+    datadir = file.path(getwd(), "report-data"),
     pages = list(default = list(title = "Default page", layout = "default", menu = NULL, components = list(), sidebar = NULL, max_components = Inf))
     )
   )
@@ -30,9 +34,13 @@ setMethod("initialize", "i2dashboard", function(.Object, ...) {
   # Do prototyping
   .Object <- callNextMethod()
 
+  # Create nice filename from title
+  if(!is.null(.Object@title)) {
+    .Object@title %>% tolower %>% gsub(pattern = " ", replacement = "-") %>% gsub(pattern = '[^a-zA-Z-]', replacement = '') %>% paste0(".Rmd") -> .Object@file
+  }
+
   # Create working directory and directory for environments
-  dir.create(.Object@workdir, showWarnings = FALSE)
-  dir.create(file.path(.Object@workdir, "envs"), recursive = T, showWarnings = FALSE)
+  dir.create(.Object@datadir, showWarnings = FALSE, recursive = T)
 
   # Validate object - tbd
   return(.Object)

inst/templates/i2dash-global-setup.Rmd

@@ -6,5 +6,8 @@ if (any(grepl(pattern = ".switchr", x = .libPaths()))) {
 
 # Make it possible to reuse chunk labels
 options(knitr.duplicate.label = "allow")
+
+# Set datadir variable, components should fetch their env from here!
+datadir <- "<% datadir %>"
 ```
 

inst/templates/vis_object.Rmd

@@ -7,6 +7,6 @@ if (!requireNamespace("<% package %>", quietly = TRUE)) {
     stop('The package <% package %> is needed to embed objects of class <% class %>.', call. = FALSE)
 }
 
-readRDS('envs/<% component_id %>.rds')
+readRDS(file.path(datadir, '<% component_id %>.rds'))
 ```
 

inst/templates/yaml_header.Rmd

+---
+title: <% title %>
+author: <% author %>
+output:
+  flexdashboard::flex_dashboard:
+    theme: <% theme %>
+<% if(interactive) sprintf('runtime: shiny') %>
+---
+<!-- This dashboard was created with the R package 'i2dash'. https://gitlab.gwdg.de/loosolab/software/i2dash -->
\ No newline at end of file

man/idashboard-class.Rd

@@ -8,9 +8,10 @@
 \alias{idashboard-class}
 \alias{add_page,i2dashboard-method}
 \alias{remove_page,i2dashboard-method}
-\title{Method to assemble a dashboard and write it to a file}
+\title{Method to assemble a dashboard to a Rmd file.}
 \usage{
-\S4method{assemble}{i2dashboard}(object, output_file, pages, ...)
+\S4method{assemble}{i2dashboard}(object, pages = names(object@pages),
+  file = object@file)
 
 \S4method{add_component}{i2dashboard,character}(object, component,
   page = "default", ...)
@@ -23,16 +24,16 @@
 \arguments{
 \item{object}{A \linkS4class{i2dash::i2dashboard} object.}
 
-\item{output_file}{The output filename (recommend that the suffix should be '.Rmd'). This file will be saved in the working directory.}
-
 \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{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{page}{The name of the page to add the component to.}
 
+\item{...}{Additional parameters passed to the components render function.}
+
 \item{title}{The title of the page to be added.}
 
 \item{layout}{The page layout (see below).}
@@ -41,8 +42,6 @@
 
 \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.}
@@ -52,7 +51,7 @@
 \item{page}{The name of the page to be removed.}
 }
 \description{
-Method to assemble a dashboard and write it to a file
+Method to assemble a dashboard to a Rmd file.
 
 Method to add a component to a page of an i2dashboard object