Adding convenience function to change params (fixes #177)

DESCRIPTION

@@ -94,6 +94,10 @@ Collate:
     'annotate_spectra.R'
     'benchmark_taxize_spectra.R'
     'calculate_entropy.R'
+    'load_yaml_files.R'
+    'go_to_cache.R'
+    'create_dir.R'
+    'change_params_small.R'
     'clean_bio.R'
     'filter_high_confidence_only.R'
     'columns_model.R'
@@ -102,7 +106,6 @@ Collate:
     'complement_metadata_structures.R'
     'copy_backbone.R'
     'create_components.R'
-    'create_dir.R'
     'create_edges.R'
     'create_edges_spectra.R'
     'decorate_bio.R'
@@ -117,7 +120,6 @@ Collate:
     'fake_lotus.R'
     'fake_sop_columns.R'
     'filter_annotations.R'
-    'go_to_cache.R'
     'get_file.R'
     'get_example_sirius.R'
     'get_example_files.R'
@@ -129,7 +131,6 @@ Collate:
     'harmonize_names_sirius.R'
     'harmonize_spectra.R'
     'install.R'
-    'load_yaml_files.R'
     'log_debug.R'
     'pre_harmonize_names_sirius.R'
     'select_annotations_columns.R'

NAMESPACE

@@ -3,6 +3,7 @@
 export(annotate_masses)
 export(annotate_spectra)
 export(calculate_mass_of_m)
+export(change_params_small)
 export(create_components)
 export(create_dir)
 export(create_edges_spectra)

NEWS.md

@@ -2,6 +2,7 @@
 
 # tima 2.11.0
 
+* Added convenience function to change small parameters (#177)
 * Added demo files download to the app
 * Better packaging
 * Improved documentation

R/change_params_small.R

@@ -0,0 +1,124 @@
+#' @title Change Params Small
+#'
+#' @description This function helps changing convenience parameters.
+#'
+#' @include create_dir.R
+#' @include get_default_paths.R
+#' @include go_to_cache.R
+#' @include load_yaml_files.R
+#'
+#' @param fil_pat The pattern identifying your whole job. You can put whatever you want. STRING
+#' @param fil_fea_raw The path to the file containing your features' intensities. Can be generated by mzmine3 or SLAW. STRING
+#' @param fil_met_raw The path to the file containing your metadata. If your experiment contains a single taxon, you can provide it below instead. STRING
+#' @param fil_sir_raw The directory containing the sirius annotations. STRING
+#' @param fil_spe_raw The path to the file containing your features' spectra. Can contain MS1 and/or MS2 spectra. STRING
+#' @param ms_pol The polarity used. Must be either "pos" or "neg". STRING
+#' @param org_tax If your experiment contains a single taxon, its scientific name. "Homo sapiens". STRING
+#' @param hig_con Filter high confidence candidates only. BOOLEAN
+#' @param summarise Summarize all candidates per feature to a single row. BOOLEAN
+#'
+#' @export
+#'
+#' @return YAML file with changed parameters.
+#'
+#' @examples
+#' \dontrun{
+#' tima:::copy_backbone()
+#' tima::change_params_small(
+#'   fil_pat = "myExamplePattern",
+#'   fil_fea_raw = "myExampleDir/myExampleFeatures.csv",
+#'   fil_met_raw = "myExampleDir2SomeWhereElse/myOptionalMetadata.tsv",
+#'   fil_sir_raw = "myExampleDir3/myAwesomeSiriusProject.zip",
+#'   fil_spe_raw = "myBeautifulSpectra.mgf",
+#'   ms_pol = "pos",
+#'   org_tax = "Gentiana lutea",
+#'   hig_con = TRUE,
+#'   summarise = FALSE
+#' )
+#' }
+change_params_small <- function(fil_pat = NULL,
+                                fil_fea_raw = NULL,
+                                fil_met_raw = NULL,
+                                fil_sir_raw = NULL,
+                                fil_spe_raw = NULL,
+                                ms_pol = NULL,
+                                org_tax = NULL,
+                                hig_con = NULL,
+                                summarise = NULL) {
+  tima:::go_to_cache()
+  paths_data_source <- tima:::get_default_paths()$data$source$path
+  paths_data_interim_annotations <-
+    tima:::get_default_paths()$data$interim$annotations$path
+  tima:::create_dir(paths_data_source)
+  list <- tima:::load_yaml_files()
+
+  yamls_params <- list$yamls_params
+  yaml_files <- list$yaml_files
+  yaml_names <- list$yaml_names
+
+  yaml_small <- yamls_params[["params/prepare_params"]]
+  if (!is.null(fil_pat)) {
+    yaml_small$files$pattern <- fil_pat
+  }
+  if (!is.null(fil_fea_raw)) {
+    stopifnot("Your features' file does not exist" = file.exists(fil_fea_raw))
+    fil_fea_raw_rdy <- paths_data_source |>
+      file.path(basename(fil_fea_raw))
+    fs::file_copy(
+      path = fil_fea_raw,
+      new_path = fil_fea_raw_rdy,
+      overwrite = TRUE
+    )
+    yaml_small$files$features$raw <- fil_fea_raw_rdy
+  }
+  if (!is.null(fil_met_raw)) {
+    stopifnot("Your metadata file does not exist" = file.exists(fil_met_raw))
+    fil_met_raw_rdy <- paths_data_source |>
+      file.path(basename(fil_met_raw))
+    fs::file_copy(
+      path = fil_met_raw,
+      new_path = fil_met_raw_rdy,
+      overwrite = TRUE
+    )
+    yaml_small$files$metadata$raw <- fil_met_raw_rdy
+  }
+  if (!is.null(fil_sir_raw)) {
+    stopifnot("Your sirius directory does not exist" = file.exists(fil_sir_raw))
+    fil_sir_raw_rdy <- paths_data_interim_annotations |>
+      file.path(basename(fil_sir_raw))
+    fs::file_copy(
+      path = fil_sir_raw,
+      new_path = fil_sir_raw_rdy,
+      overwrite = TRUE
+    )
+    yaml_small$files$annotations$raw$sirius <- fil_sir_raw_rdy
+  }
+  if (!is.null(fil_spe_raw)) {
+    stopifnot("Your spectra file does not exist" = file.exists(fil_spe_raw))
+    fil_spe_raw_rdy <- paths_data_source |>
+      file.path(basename(fil_spe_raw))
+    fs::file_copy(
+      path = fil_spe_raw,
+      new_path = fil_spe_raw_rdy,
+      overwrite = TRUE
+    )
+    yaml_small$files$spectral$raw <- fil_spe_raw_rdy
+  }
+  if (!is.null(ms_pol)) {
+    yaml_small$ms$polarity <- ms_pol
+  }
+  if (!is.null(org_tax)) {
+    yaml_small$organisms$taxon <- org_tax
+  }
+  if (!is.null(hig_con)) {
+    yaml_small$options$high_confidence <- hig_con
+  }
+  if (!is.null(summarise)) {
+    yaml_small$options$summarise <- summarise
+  }
+
+  yaml::write_yaml(
+    x = yaml_small,
+    file = tima:::get_default_paths()$params$prepare_params
+  )
+}

codemeta.json

@@ -555,7 +555,7 @@
     "SystemRequirements": null
   },
   "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
-  "fileSize": "4078.719KB",
+  "fileSize": "4086.17KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",

tests/testthat/test-functions.R

@@ -530,6 +530,21 @@ test_that(desc = "Test functions", code = {
   # tima:::.onLoad()
   # tima_full()
 
+  ## Change small params
+  get_example_files()
+  change_params_small()
+  change_params_small(
+    fil_pat = "myExamplePattern",
+    fil_fea_raw = paths$data$source$features,
+    fil_met_raw = paths$data$source$metadata,
+    fil_sir_raw = paths$data$interim$annotations$example_sirius$v6,
+    fil_spe_raw = paths$data$source$spectra,
+    ms_pol = "pos",
+    org_tax = "Gentiana lutea",
+    hig_con = TRUE,
+    summarise = FALSE
+  )
+
   ## CLI arguments check
   arguments <- character()
   arguments$ann_can_fin <- 0

vignettes/tima.Rmd

@@ -111,3 +111,19 @@ If you do not even need a GUI ☠️:
 ```{r eval=FALSE, include=TRUE}
 tima::tima_full()
 ```
+
+In case you just want to change some small parameters between jobs, a convenience function is available:
+
+```{r eval=FALSE, include=TRUE}
+tima::change_params_small(
+  fil_pat = "myExamplePattern",
+  fil_fea_raw = "myExampleDir/myExampleFeatures.csv",
+  fil_met_raw = "myExampleDir2SomeWhereElse/myOptionalMetadata.tsv",
+  fil_sir_raw = "myExampleDir3/myAwesomeSiriusProject.zip",
+  fil_spe_raw = "myBeautifulSpectra.mgf",
+  ms_pol = "pos",
+  org_tax = "Gentiana lutea",
+  hig_con = TRUE,
+  summarise = FALSE
+)
+```