update documentation

Author: ItsMeKathy

R/helpers-prototypeList.R

@@ -1,15 +1,17 @@
-#' Generates a list of graph prototypes for the different isomorphism classes and
+#' Generates a list of graph prototypes for the different isomorphism classes and their occurence.
 #'
 #'
-#' @param G graph
-#' @param sort_by_nr_edges logical, if TRUE, the list of prototypes is sorted by number of edges
+#' @param G                  \strong{igraph graph object} \cr
+#'                           A graph.
+#' @param sort_by_nr_edges   \strong{logical} \cr
+#'                           If \code{TRUE}, the list of prototypes is sorted by number of edges.
 #'
-#' @return list of prototype graphs plus count
+#' @return A list of prototype graphs plus their count.
 #' @export
 #'
 #' @examples
 #'
-#'
+
 generatePrototypeList <- function(G, sort_by_nr_edges = FALSE) {
 
 

R/helpers-small_helper_functions.R

@@ -1,12 +1,17 @@
-#' Geometric mean
+#' Calculate the geometric mean.
 #'
-#' @param x vector with numbers
-#' @param useprod if TRUE, prod(x)^(1/n) will be calculated, otherwise exp(mean(log(x)))
+#' @param x         \strong{numeric vector} \cr
+#'                  Input data.
+#' @param useprod   \strong{logical} \cr
+#'                  If \code{TRUE}, prod(x)^(1/n) will be calculated, otherwise exp(mean(log(x))).
 #'
-#' @return geometric mean of the provided data points
+#' @return The geometric mean of the provided data points.
 #' @export
 #'
-#' @examples # TODO
+#' @examples
+#' data <- c(1,6,3.5)
+#' result <- geom_mean(data, useprod = FALSE)
+
 geom_mean <- function(x, useprod = FALSE) {
   n <- length(x)
 

R/plotBipartiteGraph.R

@@ -5,23 +5,39 @@
 
 #' Plotting of bipartite peptide-protein graphs.
 #'
-#' @param G A bipartite graph (igraph object).
-#' @param vertex.label.dist Distance of the label from center of the vertex (0 = centered in vertex).
-#' @param legend Add legend?
-#' @param vertex.color Colours for the different vertex types.
-#' @param vertex.size Size of vertices.
-#' @param vertex.label.cex Size of vertex labels.
-#' @param edge.width Width of the edges.
-#' @param vertex.size2 Vertex size 2.
-#' @param useCanonicalPermutation Convert the graph into the canonical permutation before plotting?
-#' @param three_shapes Use a separate shape for the unique peptides?
-#' @param ... Additional arguments for plot.igraph.
-#' @param node_labels_proteins "letters" or "acessions"
-#' @param node_labels_peptides "numbers" or "pep_ratios" or "pep_ratio_aggr"
-#' @param round_digits Number of digits to round the peptide ratios to.
-#' @param use_edge_attributes Use edge attributes for plotting (e.g. deleted edges will be dashed)?
-#' @param legend.x x-coordinate of the legend.
-#' @param legend.y y-coordinate of the legend.
+#' @param G                         \strong{igraph graph object} \cr
+#'                                  A bipartite peptide-protein graph.
+#' @param vertex.label.dist         \strong{numeric} \cr
+#'                                  The distance of the label from center of the vertex (0 = centered in vertex).
+#' @param legend                    \strong{logical} \cr
+#'                                  If \code{TRUE}, a legend will be added.
+#' @param vertex.color              \strong{character vector} \cr
+#'                                  The colours for the different vertex types.
+#' @param vertex.size               \strong{numeric} \cr
+#'                                  The size of vertices.
+#' @param vertex.label.cex          \strong{numeric} \cr
+#'                                  The size of vertex labels.
+#' @param edge.width                \strong{numeric} \cr
+#'                                  The width of the edges.
+#' @param vertex.size2              \strong{numeric} \cr
+#'                                  The vertex size 2.
+#' @param useCanonicalPermutation   \strong{logical} \cr
+#'                                  If \code{TRUE}, the graph will be converted into the canonical permutation before plotting.
+#' @param three_shapes              \strong{logical} \cr
+#'                                  If \code{TRUE}, a separate shape will be used for the unique peptides.
+#' @param node_labels_proteins      \strong{character} \cr
+#'                                  The type of labels for the proteins. Options are "letters" or "acessions".
+#' @param node_labels_peptides      \strong{character} \cr
+#'                                  The type of labels for the peptides. Options are"numbers" or "pep_ratios" or "pep_ratio_aggr".
+#' @param round_digits              \strong{integer} \cr
+#'                                  The number of digits to round the peptide ratios to.
+#' @param use_edge_attributes       \strong{logical} \cr
+#'                                  If \code{TRUE}, edge attributes will be used for plotting (e.g. deleted edges will be dashed)
+#' @param legend.x                  \strong{numeric or character} \cr
+#'                                  The x-coordinate of the legend or a keyword for the position. See [graphics::legend()] for details.
+#' @param legend.y                  \strong{numeric or character} \cr
+#'                                  The y-coordinate of the legend or a keyword for the position. See [graphics::legend()] for details.
+#' @param ...                       Additional arguments for plot.igraph.
 #'
 #' @return Plot of one bipartite graph.
 #' @export
@@ -30,6 +46,7 @@
 #' biadjacency_matrix <- matrix(c(1,1,1,0), nrow = 2)
 #' G <- igraph::graph_from_biadjacency_matrix(biadjacency_matrix)
 #' #plotBipartiteGraph(G, three_shapes = TRUE, useCanonicalPermutation = TRUE)
+
 plotBipartiteGraph <- function(G, vertex.label.dist = 0, legend = TRUE,
                                vertex.color = c("mediumseagreen", "cadetblue2", "coral1"),
                                vertex.size = 15, vertex.label.cex = 1, edge.width = 1, vertex.size2=15,

R/tables-subgraph_characteristics.R

@@ -1,17 +1,21 @@
-
 #' Generates a table with characteristics for each subgraph in a list.
 #'
-#' @param S list of subgraphs, where peptide and protein nodes are collapsed
-#' @param fastalevel Are the subgraphs on fasta level?
-#' @param prototype Are the subgraphs part of a prototype list?
-#' @param file where to save the table.
+#' @param S            \strong{list of igraph graph objects} \cr
+#'                     A list of subgraphs, where peptide and protein nodes are collapsed.
+#' @param fastalevel   \strong{logical} \cr
+#'                     If \code{TRUE}, the subgraphs should be on fasta level
+#' @param prototype    \strong{logical} \cr
+#'                     If \code{TRUE}, the subgraphs should be part of a prototype list
+#' @param file         \strong{character} \cr
+#'                     A file path where to save the table.
 #'
 #'
-#' @return table
+#' @return A table with the characteristics.
 #' @export
 #'
 #' @examples
-#' # TODO
+#'
+
 calculate_subgraph_characteristics <- function(S, #S2, S3,
                                                fastalevel = TRUE,
                                                prototype = FALSE,

R/tables-summary_table_graphs.R

@@ -1,12 +1,16 @@
-
 #' Calculate number for table
-#' @param subgraph_char_tab subgraphs characteristics tables
-#' @param isomorph_list isomorph lists
+#'
+#' @param subgraph_char_tab   \strong{data.frame} \cr
+#'                            A table of subgraphs characteristics, e.g. created by [calculate_subgraph_characteristics()]
+#' @param isomorph_list       \strong{list} \cr
+#'                            A list of occuring isomorphs.
 #'
 #' @return bla
 #' @export
 #'
-#' @examples # TODO
+#' @examples
+#'
+
 calculate_summary_table <- function(subgraph_char_tab, isomorph_list) {
 
   D <- subgraph_char_tab