Merge pull request #10 from mpc-bioinformatics/documentation

Some docu as well as updating the automated testing.

Author: ItsMeKathy

.github/workflows/test-coverage.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, documentation]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, documentation]
 
 name: test-coverage
 
@@ -44,7 +44,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,9 +1,10 @@
 Package: bppg
 Title: Bipartite peptide-protein graphs
 Version: 0.0.0.9000
-Authors@R: 
+Authors@R: c(
     person("Karin", "Schork", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0003-3756-4347"))
+           comment = c(ORCID = "0000-0003-3756-4347")),
+    person("Katharina", "Neuhaus", , "[email protected]", role = c("aut")))
 Description: Functionality to create and characterize bipartite graphs that 
     show the relationship between peptides and proteins in bottom-up proteomics.
 License: BSD_3_clause + file LICENSE

R/generate_graphs_from_FASTA.R

@@ -1,13 +1,20 @@
 #' Generate graphs from a FASTA file
 #'
-#' @param fasta fasta file, already read into R by seqinr::read.fasta
-#' @param collapse_protein_nodes collapse protein nodes?
-#' @param collapse_peptide_nodes collapse peptide nodes?
-#' @param result_path path where results are saved. If NULL, results are not saved
-#' @param suffix suffix for saving results
-#' @param save_intermediate Save intermediate results?
-#' @param ... additional arguments to bppg::digest_fasta()
-#' @param prot_origin origin of protein, e.g. organism etc.
+#' @param fasta                    \strong{list of vector of chars} \cr
+#'                                 A fasta file, already read into R by seqinr::read.fasta().
+#' @param collapse_protein_nodes   \strong{logical} \cr
+#'                                 If \code{TRUE}, the protein nodes will be collapsed.
+#' @param collapse_peptide_nodes   \strong{logical} \cr
+#'                                 If \code{TRUE}, the peptide nodes will be collapsed.
+#' @param result_path              \strong{character} \cr
+#'                                 The path where results are saved. If \code{NULL}, results are not saved.
+#' @param suffix                   \strong{character} \cr
+#'                                 The suffix for saving results.
+#' @param save_intermediate        \strong{logical} \cr
+#'                                 If \code{TRUE}, the intermediate results will also be saved.
+#' @param prot_origin              \strong{character vector} \cr
+#'                                 The origin of protein, e.g. organism etc.
+#' @param ...                      Additional arguments to bppg::digest_fasta()
 #'
 #' @return subgraphs (i.e. connected components) from the graph generated from the FASTA file.
 #' @export
@@ -18,10 +25,13 @@
 #' fasta <- seqinr::read.fasta(file = file, seqtype = "AA", as.string = TRUE)
 #' graphs <- bppg::generate_graphs_from_FASTA(fasta)
 #'
-generate_graphs_from_FASTA <- function(fasta, collapse_protein_nodes = TRUE,
+
+generate_graphs_from_FASTA <- function(fasta,
+                                       collapse_protein_nodes = TRUE,
                                        collapse_peptide_nodes = TRUE,
                                        result_path = NULL,
-                                       suffix = NULL, save_intermediate = FALSE,
+                                       suffix = NULL,
+                                       save_intermediate = FALSE,
                                        prot_origin = NULL,
                                        ...) {
 

R/generate_graphs_from_quantdata.R

@@ -1,20 +1,38 @@
-#' Generate graphs from peptide ratio table, using an edgelist calculated on the fasta file
+#' Generate graphs from peptide ratio table, using an edgelist calculated on the fasta file.
 #'
-#' @param peptide_ratios table with peptide ratios
-#' @param id_cols columns with ids, e.g. peptide sequences (everything except the peptide ratios)
-#' @param fasta_edgelist Edgelist created from the corresponding FASTA file
-#' @param outpath output path
-#' @param seq_column column name of the peptide sequence
-#' @param collapse_protein_nodes if TRUE protein nodes will be collapsed
-#' @param collapse_peptide_nodes if TRUE, peptide nodes will be collapsed
-#' @param suffix suffix for output files
+#' @param peptide_ratios           \strong{data.frame} \cr
+#'                                 A table with peptide ratios.
+#' @param id_cols                  \strong{integer vector} \cr
+#'                                 The columns with ids, e.g. peptide sequences (everything except the peptide ratios)
+#' @param fasta_edgelist           \strong{data.frame} \cr
+#'                                 An edgelist created from the corresponding FASTA file, eg. created with [generate_edgelist()].
+#' @param outpath                  \strong{character} \cr
+#'                                 The output path for the results.
+#' @param seq_column               \strong{character} \cr
+#'                                 The column name of the peptide sequence.
+#' @param collapse_protein_nodes   \strong{logical} \cr
+#'                                 If \code{TRUE}, the protein nodes will be collapsed.
+#' @param collapse_peptide_nodes   \strong{logical} \cr
+#'                                 If \code{TRUE}, the peptide nodes will be collapsed.
+#' @param suffix                   \strong{character} \cr
+#'                                 The suffix for saving results.
 #'
-#' @return list of list of subgraphs
+#' @return A list of list of subgraphs
 #' @export
 #'
+#' @seealso [generate_edgelist()]
+#'
 #' @examples
-generate_quant_graphs <- function(peptide_ratios, id_cols = 1, fasta_edgelist, outpath = NULL, seq_column = "Sequence",
-                                  collapse_protein_nodes = TRUE, collapse_peptide_nodes = FALSE, suffix = "") {
+#'
+
+generate_quant_graphs <- function(peptide_ratios,
+                                  id_cols = 1,
+                                  fasta_edgelist,
+                                  outpath = NULL,
+                                  seq_column = "Sequence",
+                                  collapse_protein_nodes = TRUE,
+                                  collapse_peptide_nodes = FALSE,
+                                  suffix = "") {
 
   ### broad filtering for edgelist for only quantifies peptides
   edgelist_filtered <- fasta_edgelist[fasta_edgelist[,2] %in% peptide_ratios[,seq_column], ]

bppg.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 0c04aeda-ae5b-4b31-800f-043d497776fc
 
 RestoreWorkspace: No
 SaveWorkspace: No