Improve app

taxonomicallyinformedannotation · Aug 15, 2024 · 8fcab5e · 8fcab5e
1 parent 4291cc5
commit 8fcab5e
Show file tree

Hide file tree

Showing 43 changed files with 85 additions and 1 deletion.
diff --git a/R/annotate_masses.R b/R/annotate_masses.R
@@ -37,6 +37,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' github <- "https://raw.githubusercontent.com/"
@@ -54,6 +55,7 @@
 #' str_tax_npc = paste0(dir, "libraries/sop/merged/structures/taxonomies/npc.tsv")
 #' )
 #' unlink("data", recursive = TRUE)
+#' }
 annotate_masses <-
  function(features = get_params(step = "annotate_masses")$files$features$prepared,
  output_annotations = get_params(step = "annotate_masses")$files$annotations$prepared$structural$ms1,

diff --git a/R/annotate_spectra.R b/R/annotate_spectra.R
@@ -25,6 +25,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' get_file(
@@ -39,6 +40,7 @@
 #' library = get_default_paths()$data$source$libraries$spectra$exp$with_rt
 #' )
 #' unlink("data", recursive = TRUE)
+#' }
 annotate_spectra <- function(input = get_params(step = "annotate_spectra")$files$spectral$raw,
  library = get_params(step = "annotate_spectra")$files$libraries$spectral,
  polarity = get_params(step = "annotate_spectra")$ms$polarity,

diff --git a/R/create_components.R b/R/create_components.R
@@ -12,6 +12,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' github <- "https://raw.githubusercontent.com/"
@@ -25,6 +26,7 @@
 #' )
 #' create_components()
 #' unlink("data", recursive = TRUE)
+#' }
 create_components <-
  function(input = get_params(step = "create_components")$files$networks$spectral$edges$prepared,
  output = get_params(step = "create_components")$files$networks$spectral$components$raw) {

diff --git a/R/create_edges_spectra.R b/R/create_edges_spectra.R
@@ -21,6 +21,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' get_file(
@@ -29,6 +30,7 @@
 #' )
 #' create_edges_spectra()
 #' unlink("data", recursive = TRUE)
+#' }
 create_edges_spectra <- function(input = get_params(step = "create_edges_spectra")$files$spectral$raw,
  output = get_params(step = "create_edges_spectra")$files$networks$spectral$edges$raw,
  name_source = get_params(step = "create_edges_spectra")$names$source,

diff --git a/R/filter_annotations.R b/R/filter_annotations.R
@@ -15,6 +15,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' github <- "https://raw.githubusercontent.com/"
@@ -47,6 +48,7 @@
 #' rts = rts
 #' )
 #' unlink("data", recursive = TRUE)
+#' }
 filter_annotations <-
  function(annotations = get_params(step = "filter_annotations")$files$annotations$prepared$structural,
  features = get_params(step = "filter_annotations")$files$features$prepared,

diff --git a/R/get_params.R b/R/get_params.R
@@ -14,9 +14,11 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' get_params("prepare_params")
+#' }
 get_params <- function(step) {
  paths <- get_default_paths()
  steps <-

diff --git a/R/prepare_annotations_gnps.R b/R/prepare_annotations_gnps.R
@@ -18,10 +18,12 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' prepare_annotations_gnps()
 #' unlink("data", recursive = TRUE)
+#' }
 prepare_annotations_gnps <-
  function(input = get_params(step = "prepare_annotations_gnps")$files$annotations$raw$spectral$gnps,
  output = get_params(step = "prepare_annotations_gnps")$files$annotations$prepared$structural$gnps,

diff --git a/R/prepare_annotations_sirius.R b/R/prepare_annotations_sirius.R
@@ -26,10 +26,12 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' prepare_annotations_sirius()
 #' unlink("data", recursive = TRUE)
+#' }
 prepare_annotations_sirius <-
  function(input_directory = get_params(step = "prepare_annotations_sirius")$files$annotations$raw$sirius,
  output_ann = get_params(step = "prepare_annotations_sirius")$files$annotations$prepared$structural$sirius,

diff --git a/R/prepare_annotations_spectra.R b/R/prepare_annotations_spectra.R
@@ -19,6 +19,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' github <- "https://raw.githubusercontent.com/"
@@ -42,6 +43,7 @@
 #' str_tax_npc = paste0(dir, "libraries/sop/merged/structures/taxonomies/npc.tsv")
 #' )
 #' unlink("data", recursive = TRUE)
+#' }
 prepare_annotations_spectra <-
  function(input = get_params(step = "prepare_annotations_spectra")$files$annotations$raw$spectral$spectral,
  output = get_params(step = "prepare_annotations_spectra")$files$annotations$prepared$structural$spectral,

diff --git a/R/prepare_features_components.R b/R/prepare_features_components.R
@@ -13,6 +13,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' github <- "https://raw.githubusercontent.com/"
@@ -24,6 +25,7 @@
 #' input = input
 #' )
 #' unlink("data", recursive = TRUE)
+#' }
 prepare_features_components <-
  function(input = get_params(step = "prepare_features_components")$files$networks$spectral$components$raw,
  output = get_params(step = "prepare_features_components")$files$networks$spectral$components$prepared) {

diff --git a/R/prepare_features_edges.R b/R/prepare_features_edges.R
@@ -14,6 +14,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' github <- "https://raw.githubusercontent.com/"
@@ -27,6 +28,7 @@
 #' input = list("ms1" = input_1, "spectral" = input_2)
 #' )
 #' unlink("data", recursive = TRUE)
+#' }
 prepare_features_edges <-
  function(input = get_params(step = "prepare_features_edges")$files$networks$spectral$edges$raw,
  output = get_params(step = "prepare_features_edges")$files$networks$spectral$edges$prepared,

diff --git a/R/prepare_features_tables.R b/R/prepare_features_tables.R
@@ -16,6 +16,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' get_file(
@@ -24,6 +25,7 @@
 #' )
 #' prepare_features_tables()
 #' unlink("data", recursive = TRUE)
+#' }
 prepare_features_tables <-
  function(features = get_params(step = "prepare_features_tables")$files$features$raw,
  output = get_params(step = "prepare_features_tables")$files$features$prepared,

diff --git a/R/prepare_libraries_rt.R b/R/prepare_libraries_rt.R
@@ -25,10 +25,12 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' prepare_libraries_rt()
 #' unlink("data", recursive = TRUE)
+#' }
 prepare_libraries_rt <-
  function(mgf_exp = get_params(step = "prepare_libraries_rt")$files$libraries$temporal$exp$mgf,
  mgf_is = get_params(step = "prepare_libraries_rt")$files$libraries$temporal$is$mgf,

diff --git a/R/prepare_libraries_sop_closed.R b/R/prepare_libraries_sop_closed.R
@@ -13,10 +13,12 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' prepare_libraries_sop_closed()
 #' unlink("data", recursive = TRUE)
+#' }
 prepare_libraries_sop_closed <-
  function(input = get_params(step = "prepare_libraries_sop_closed")$files$libraries$sop$raw$closed,
  output = get_params(step = "prepare_libraries_sop_closed")$files$libraries$sop$prepared$closed) {

diff --git a/R/prepare_libraries_sop_ecmdb.R b/R/prepare_libraries_sop_ecmdb.R
@@ -13,10 +13,12 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' prepare_libraries_sop_ecmdb()
 #' unlink("data", recursive = TRUE)
+#' }
 prepare_libraries_sop_ecmdb <-
  function(input = get_params(step = "prepare_libraries_sop_ecmdb")$files$libraries$sop$raw$ecmdb,
  output = get_params(step = "prepare_libraries_sop_ecmdb")$files$libraries$sop$prepared$ecmdb) {

diff --git a/R/prepare_libraries_sop_hmdb.R b/R/prepare_libraries_sop_hmdb.R
@@ -15,10 +15,12 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' prepare_libraries_sop_hmdb()
 #' unlink("data", recursive = TRUE)
+#' }
 prepare_libraries_sop_hmdb <-
  function(input = get_params(step = "prepare_libraries_sop_hmdb")$files$libraries$sop$raw$hmdb,
  output = get_params(step = "prepare_libraries_sop_hmdb")$files$libraries$sop$prepared$hmdb) {

diff --git a/R/prepare_libraries_sop_lotus.R b/R/prepare_libraries_sop_lotus.R
@@ -15,10 +15,12 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' prepare_libraries_sop_lotus()
 #' unlink("data", recursive = TRUE)
+#' }
 prepare_libraries_sop_lotus <-
  function(input = get_params(step = "prepare_libraries_sop_lotus")$files$libraries$sop$raw$lotus,
  output = get_params(step = "prepare_libraries_sop_lotus")$files$libraries$sop$prepared$lotus) {

diff --git a/R/prepare_libraries_sop_merged.R b/R/prepare_libraries_sop_merged.R
@@ -29,6 +29,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' github <- "https://raw.githubusercontent.com/"
@@ -43,6 +44,7 @@
 #' get_file(url = paste0(dir, files), export = files)
 #' prepare_libraries_sop_merged(files = files)
 #' unlink("data", recursive = TRUE)
+#' }
 prepare_libraries_sop_merged <-
  function(files = get_params(step = "prepare_libraries_sop_merged")$files$libraries$sop$prepared,
  filter = get_params(step = "prepare_libraries_sop_merged")$organisms$filter$mode,

diff --git a/R/prepare_libraries_spectra.R b/R/prepare_libraries_spectra.R
@@ -36,10 +36,12 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' prepare_libraries_spectra()
 #' unlink("data", recursive = TRUE)
+#' }
 prepare_libraries_spectra <-
  function(input = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$raw,
  nam_lib = get_params(step = "prepare_libraries_spectra")$names$libraries,

diff --git a/R/prepare_taxa.R b/R/prepare_taxa.R
@@ -31,6 +31,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' github <- "https://raw.githubusercontent.com/"
@@ -52,6 +53,7 @@
 #' org_tax_ott = org_tax_ott
 #' )
 #' unlink("data", recursive = TRUE)
+#' }
 prepare_taxa <-
  function(input = get_params(step = "prepare_taxa")$files$features$raw,
  extension = get_params(step = "prepare_taxa")$names$extension,

diff --git a/R/weight_annotations.R b/R/weight_annotations.R
@@ -90,6 +90,7 @@
 #' @seealso annotate_masses weight_bio weight_chemo
 #'
 #' @examples
+#' \donttest{
 #' tima:::copy_backbone()
 #' go_to_cache()
 #' github <- "https://raw.githubusercontent.com/"
@@ -170,6 +171,7 @@
 #' taxa = taxa
 #' )
 #' unlink("data", recursive = TRUE)
+#' }
 weight_annotations <- function(library = get_params(step = "weight_annotations")$files$libraries$sop$merged$keys,
  org_tax_ott = get_params(step = "weight_annotations")$files$libraries$sop$merged$organisms$taxonomies$ott,
  str_stereo = get_params(step = "weight_annotations")$files$libraries$sop$merged$structures$stereo,

diff --git a/codemeta.json b/codemeta.json
@@ -506,7 +506,7 @@
  "SystemRequirements": null
  },
  "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
- "fileSize": "3253.523KB",
+ "fileSize": "3254.195KB",
  "citation": [
  {
  "@type": "SoftwareSourceCode",

diff --git a/man/annotate_masses.Rd b/man/annotate_masses.Rd
diff --git a/man/annotate_spectra.Rd b/man/annotate_spectra.Rd
diff --git a/man/create_components.Rd b/man/create_components.Rd
diff --git a/man/create_edges_spectra.Rd b/man/create_edges_spectra.Rd
diff --git a/man/filter_annotations.Rd b/man/filter_annotations.Rd
diff --git a/man/get_params.Rd b/man/get_params.Rd