Added links in doc + updated template functions

NEWS.md

@@ -0,0 +1 @@
+# moiraine (development version)

R/template_report.R

@@ -1,169 +1,41 @@
-#' Creates Rmd report from template
-#'
-#' Creates a Rmarkdown report to present the results from the integration analysis.
-#' This function only creates a `.Rmd` file and does not knit the document.
-#'
-#' @param file Name (and path) of the file to be created. Should end with `.Rmd`
-#' if `use_quarto` is `FALSE`, or `.qmd` if `use_quarto` is `TRUE`.
-#' @param add_sections Character vector, names of the sections to include in the
-#' report. Possible values are 'spls', 'so2pls', 'mofa', 'diablo' and 'comparison'.
-#' By default, all sections are included.
-#' @param overwrite Logical, should existing file be overwritten?
-#' @param target_project Character, name of the current targets project (i.e. value to be used for
-#' the `TAR_PROJECT` environment variable). If none provided, will be read from the `TAR_PROJECT`
-#' environment variable or set to `"main"` if the former is not set.
-#' @param use_quarto Boolean, whether to use a Quarto report. Default value is `FALSE`, i.e.
-#' uses a Rmarkdown report.
-#' @return Invisible character, the path and name of the generated `.Rmd` (or `.qmd`) file.
-#' @export
-create_report <- function(file,
-                          add_sections = c("spls", "so2pls", "mofa", "diablo", "comparison"),
-                          overwrite = FALSE,
-                          target_project = Sys.getenv("TAR_PROJECT", "main"),
-                          use_quarto = FALSE) {
-  if (use_quarto) {
-    if (!stringr::str_detect(file, "\\.qmd$")) stop("'file' argument should end with '.qmd'.")
-    prefix <- "quarto_"
-    ext <- ".qmd"
-  } else {
-    if (!stringr::str_detect(file, "\\.Rmd$")) stop("'file' argument should end with '.Rmd'.")
-    prefix <- ""
-    ext <- ".Rmd"
-  }
-
-
-  ## Check that the path to file is valid
-  dir_name <- dirname(file)
-  if (!file.exists(dir_name)) stop("Directory '", dir_name, "' does not exist.")
-
-  ## Check whether the file already exists
-  if (file.exists(file) & !overwrite) stop("File '", file, "' already exists. Use 'overwrite = TRUE' to overwrite it.")
-
-  ## Copy the content of the template Rmd report
-  report_template_file <- system.file("templates", paste0(prefix, "report_template", ext), package = "moiraine")
-  lines_text <- readLines(report_template_file)
-
-  to_replace <- c(
-    "_REPORT_FILE_PATH_" = file,
-    "_TARGETS_PROJECT_" = target_project
-  )
-
-  out_lines <- lines_text
-
-  for (i in names(to_replace)) {
-    out_lines <- gsub(
-      i,
-      to_replace[i],
-      out_lines
-    )
-  }
-
-  .check_names(
-    add_sections,
-    c("spls", "so2pls", "mofa", "diablo", "comparison"),
-    "In 'add_sections' argument, the following section names are not recognised: '_W_'. Possible section names are: '_C_'."
-  )
-
-  for (i in add_sections) {
-    template_file <- system.file("templates", paste0(prefix, "fragment_report_", i, "_template", ext), package = "moiraine")
-    lines_template <- readLines(template_file)
-    out_lines <- c(out_lines, lines_template)
-  }
-
-  writeLines(out_lines, file)
-  message("File '", file, "' created.\n")
-
-  return(invisible(file))
-}
-
 #' Creates a target script file from template
 #'
-#' Creates a target script file form a template multi-omics integration pipeline.
-#' This function only creates the script file but does not execute it.
+#' Creates a target script file form a template multi-omics integration
+#' pipeline. This function only creates the script file but does not execute it.
 #'
 #' @param file Name (and path) of the file to be created. Should end with `.R`.
-#' Default value (recommended) is `"_targets.R"` (in the current directory).
+#'   Default value (recommended) is `"_targets.R"` (in the current directory).
 #' @param overwrite Logical, should existing file be overwritten?
 #' @return The file name (invisibly).
-#' @export
-create_targets_pipeline <- function(file = "_targets.R", overwrite = FALSE) {
-  if (!stringr::str_detect(file, "\\.R$")) stop("'file' argument should end with '.R'.")
+#' @exports
+create_moiraine_pipeline <- function(file = "_targets.R", overwrite = FALSE) {
+  if (!stringr::str_detect(file, "\\.R$")) {
+    stop("'file' argument should end with '.R'.")
+  }
 
   ## Check that the path to file is valid
   dir_name <- dirname(file)
-  if (!file.exists(dir_name)) stop("Directory '", dir_name, "' does not exist.")
+  if (!file.exists(dir_name)) {
+    stop("Directory '", dir_name, "' does not exist.")
+  }
 
   ## Check whether the file already exists
-  if (file.exists(file) & !overwrite) stop("File '", file, "' already exists. Use 'overwrite = TRUE' to overwrite it.")
+  if (file.exists(file) & !overwrite) {
+    stop("File '",
+         file,
+         "' already exists. Use 'overwrite = TRUE' to overwrite it.")
+  }
 
   ## Get the template targets file
-  targets_template_file <- system.file("templates", "template_target.R", package = "moiraine")
+  targets_template_file <- system.file(
+    "templates",
+    "template_target_minimal.R",
+    package = "moiraine"
+  )
 
   file.copy(targets_template_file, file, overwrite = overwrite)
 
   message("File '", file, "' created.\n")
 
   return(invisible(file))
 }
-
-#' Make Quarto report template from Rmd template
-#'
-#' Generates the Quarto report templates from corresponding Rmd report
-#' templates.
-#'
-#' @noRd
-.make_quarto_template <- function() {
-  ## Constructing template for report header and first part
-  main_rmd <- here::here("inst/templates/report_template.Rmd")
-
-  main_rmd_con <- file(main_rmd, "r")
-  main_rmd_lines <- readLines(main_rmd_con)
-  close(main_rmd_con)
-
-  yaml_header_end <- which(main_rmd_lines == "---")[2]
-  yaml_header <- main_rmd_lines[seq_len(yaml_header_end)]
-  content <- main_rmd_lines[-seq_len(yaml_header_end)]
-
-  yaml_header[yaml_header == "date: '`r format(Sys.Date(), \"%B %d, %Y\")`'"] <- "date: today"
-  yaml_header[yaml_header == "output:"] <- "format:"
-  yaml_header[yaml_header == "  html_document:"] <- "  html:"
-  yaml_header <- yaml_header[!(yaml_header %in% c("     toc_float: true", "     theme: flatly"))]
-
-  tmp <- which(yaml_header == "  html:")
-  yaml_header <- c(
-    yaml_header[seq_len(tmp)],
-    "     toc-location: right",
-    "     embed-resources: true",
-    yaml_header[-seq_len(tmp)]
-  )
-
-  content <- content |>
-    stringr::str_remove_all(" \\{\\.tabset \\.tabset-pills\\}") |>
-    stringr::str_remove_all(" \\{\\.active\\}")
-
-  main_qmd <- here::here("inst/templates/quarto_report_template.qmd")
-  main_qmd_con <- file(main_qmd, "w")
-  writeLines(c(yaml_header, content), con = main_qmd_con)
-  close(main_qmd_con)
-
-  dir("inst/templates/", pattern = "fragment.+Rmd") |>
-    purrr::walk(
-      function(.x) {
-        file_con <- file(here::here("inst/templates", .x), "r")
-        content <- readLines(file_con)
-        close(file_con)
-
-        content <- content |>
-          stringr::str_remove_all(" \\{\\.tabset \\.tabset-pills\\}") |>
-          stringr::str_remove_all(" \\{\\.active\\}")
-
-        new_file <- paste0(
-          "quarto_",
-          stringr::str_replace(.x, "\\.Rmd$", ".qmd")
-        )
-        new_file_con <- file(here::here("inst/templates", new_file), "w")
-        writeLines(content, con = new_file_con)
-        close(new_file_con)
-      }
-    )
-}

README.Rmd

@@ -39,15 +39,14 @@ devtools::install_github("PlantandFoodResearch/moiraine")
 
 ## Example
 
-To get started, create a new analysis pipeline and associated report in your working directory with:
+To get started, create a new analysis pipeline in your working directory with:
 
 ```{r example}
 #| eval: false
 
 library(moiraine)
 
-create_targets_pipeline()
-create_report("integration_analysis_report.Rmd")
+create_moiraine_pipeline()
 ```
 
 Before using `moiraine`, we encourage you to get familiar with the `targets` package; the [manual](https://books.ropensci.org/targets/) is a great place to start.

README.md

@@ -36,14 +36,13 @@ devtools::install_github("PlantandFoodResearch/moiraine")
 
 ## Example
 
-To get started, create a new analysis pipeline and associated report in
-your working directory with:
+To get started, create a new analysis pipeline in your working directory
+with:
 
 ``` r
 library(moiraine)
 
-create_targets_pipeline()
-create_report("integration_analysis_report.Rmd")
+create_moiraine_pipeline()
 ```
 
 Before using `moiraine`, we encourage you to get familiar with the

_pkgdown.yml

@@ -2,12 +2,25 @@ url: https://bookish-disco-p832pyq.pages.github.io/
 template:
   bootstrap: 5
 
+navbar:
+  title: targets
+  type: default
+  left:
+  - text: Reference
+    href: reference/index.html
+  - text: Manual
+    href: https://solid-lamp-kq546rq.pages.github.io/
+  - text: News
+    href: news/index.html
+  right:
+  - icon: fa-github fa-lg
+    href: https://github.com/PlantandFoodResearch/moiraine
+
 reference:
 - title: "Project management"
   desc: "Getting started with a new data integration project"
   contents:
-  - create_targets_pipeline
-  - create_report
+  - create_moiraine_pipeline
 
 - title: "Data import"
   desc: "Importing data into R"
@@ -81,6 +94,7 @@ reference:
   - transformation_datasets_factory
   - get_transformed_data
   - get_table_transformations
+  - zero_to_half_min
 
 - title: "Prefiltering"
   desc: "Features prefiltering for multi-omics set"