R/addIsoAssign.R

In jasenfinch/MFassign: Molecular Formula Assignment For High Resolution ESI-MS Based Metabolomics Data

#' @rdname assignment-methods
#' @export

setGeneric("addIsoAssign", function(assignment)
  standardGeneric("addIsoAssign")
)

#' @rdname assignment-methods
#' @importFrom dplyr arrange rowwise slice_sample left_join ungroup anti_join
#' @importFrom stringr str_detect
#' @importFrom mzAnnotation calcM ipMF
#' @importFrom igraph vertex.attributes V
#' @importFrom furrr furrr_options
#' @importFrom methods as

setMethod('addIsoAssign',signature = 'Assignment',
          function(assignment){
            
            invisible(gc())
            
            rel <- assignment %>% 
              relationships()
            
            if (ncol(rel) == 0){
              stop('No relationships found. Has `calcRelationships()` been called on this object?',
                   call. = FALSE)
            }
            
            if (isTRUE(assignment@log$verbose)) {
              ai_start_time <- proc.time()
              message(blue('Adduct & isotopic assignment '),
                      cli::symbol$continue)
            }
            
            assignment_technique <- technique(assignment)
            
            if (str_detect(assignment_technique,'LC')){
              rel <- rel %>% 
                filter(RetentionTimeDiff <= assignment@RT_diff_limit)
            }
            
            rel <- rel %>% 
              filter(is.na(Transformation1) & 
                       is.na(Transformation2) & 
                       coefficient > 0) %>%
              filter(!(is.na(Isotope1) & 
                         !is.na(Isotope2) & 
                         Adduct1 == Adduct2 & 
                         log2IntensityRatio < 0)) %>%
              filter(!(!is.na(Isotope1) & 
                         is.na(Isotope2) & 
                         Adduct1 == Adduct2)) 
            
            M <- collateM(rel,
                          maxM(assignment))
            
            if (isTRUE(assignment@log$verbose)) {
              start_time <- proc.time()
              message('generating molecular formulas',
                      cli::symbol$continue,
                      '\r',
                      appendLF = FALSE)
            }
            
            MFs <- generateMFs(M,
                               ppm(assignment),
                               MFrankThreshold(assignment),
                               adductRules(assignment),
                               isotopeRules(assignment),
                               AIS(assignment))
            
            if (isTRUE(assignment@log$verbose)) {
              end_time <- proc.time()
              elapsed <- elapsedTime(start_time,end_time)
              message('generating molecular formulas',
                      '\t',
                      green(cli::symbol$tick),
                      ' ',
                      elapsed)
            }
            
            graph_edges <- rel %>% 
              addMFs(MFs) %>%
              filter(MF1 == MF2) %>%
              mutate(RetentionTime1 = as.numeric(RetentionTime1),
                     RetentionTime2 = as.numeric(RetentionTime2)) %>%
              addNames()
            
            graph_nodes <- collateMFs(graph_edges,MFs)
            
            graph <- calcComponents(graph_nodes,
                                    graph_edges,
                                    assignment)
            
            counter <- 0
            
            repeat {
              
              counter <- counter + 1
              
              if (isTRUE(assignment@log$verbose)) {
                start_time <- proc.time()
                message(paste0('iteration ',counter),
                        cli::symbol$continue,
                        '\r',
                        appendLF = FALSE)
              }
              
              if (counter > 1){
                graph <- assignment@addIsoAssign[[counter - 1]]$graph %>% 
                  activate(nodes) %>% 
                  anti_join(assignment %>% 
                              assignments() %>% 
                              select(dplyr::any_of(c('Feature','Isotope','Adduct','MF'))),
                            by = 'Feature') 
                
                if (nrow(edges(graph)) == 0) break() 
                
                graph <- graph %>% 
                  clean(adductRules(assignment)) %>% 
                  recalcComponents(assignment)
              }
              
              filtered_graph <- graph 
              
              filtered_graph <- filtered_graph %>% 
                filterComponents(assignment,
                                 filters = componentFilters())
              
              assigned_features <- filtered_graph %>% 
                nodes() %>% 
                rename(Name = name) %>%
                mutate(Mode = str_sub(Feature,1,1))
              
              if (nrow(assigned_features) == 0) break()
              
              assignment@addIsoAssign[[counter]] <- list(
                graph = graph,
                filtered_graph = filtered_graph,
                assigned = assigned_features
              )
              
              assignment@assignments <- bind_rows(
                assignment@assignments,
                assigned_features %>%
                  select(Name:`MF Plausibility (%)`,
                         Mode,
                         Component) %>%
                  mutate(Iteration = paste0('A&I',counter))
              )
              
              if (isTRUE(assignment@log$verbose)) {
                end_time <- proc.time()
                elapsed <- elapsedTime(start_time,end_time)
                message(paste0('iteration ',counter),
                        '\t\t\t',
                        green(cli::symbol$tick),
                        ' ',
                        elapsed)
              }
              
            }
            
            names(assignment@addIsoAssign) <- paste0('A&I',
                                                     seq_along(assignment@addIsoAssign))
            
            if (isTRUE(assignment@log$verbose)) {
              ai_end_time <- proc.time()
              elapsed <- elapsedTime(ai_start_time,
                                     ai_end_time)
              message(blue('Adduct & isotopic assignment '),'\t',green(cli::symbol$tick),' ',elapsed)
            }
            
            return(assignment)
          })