Mercurial > repos > lain > xseekerpreparator

comparison galaxy/tools/LC-MSMS/XSeekerPreparator.R @ 12:bdb2878ee189 draft

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" master branch Updating"
author lain
date Wed, 07 Apr 2021 13:05:36 +0000
parents f4fc4a0f41e2
children 26f01380145d
comparison
equal deleted inserted replaced
11:f4fc4a0f41e2 12:bdb2878ee189
482 context$groupidx <- rdata$xa@xcmsSet@groupidx 482 context$groupidx <- rdata$xa@xcmsSet@groupidx
483 xcms_set <- rdata$xa@xcmsSet 483 xcms_set <- rdata$xa@xcmsSet
484 singlefile <- rdata$singlefile 484 singlefile <- rdata$singlefile
485 process_arg_list <- rdata$listOFlistArguments 485 process_arg_list <- rdata$listOFlistArguments
486 var_meta <- rdata$variableMetadata 486 var_meta <- rdata$variableMetadata
487 ## We needed to get rid of the rdata, which is very big.
488 ## So we gathered all variable assignment from rdata here, and got rid of it.
489 rm(rdata)
490 487
491 process_params <- list() 488 process_params <- list()
492 for (list_name in names(process_arg_list)) { 489 if (is.null(process_arg_list)) {
493 param_list <- list() 490 histories <- list()
494 for (param_name in names(process_arg_list[[list_name]])) { 491 for (history in xcms_set@.processHistory) {
495 param_list[[param_name]] <- process_arg_list[[list_name]][[param_name]] 492 if (
496 } 493 class(history@param) == "CentWaveParam"
497 process_params[[length(process_params)+1]] <- param_list 494 && history@type == "Peak detection"
498 } 495 ) {
496 params <- history@param
497 process_params <- list(list(
498 xfunction="annotatediff",
499 ppm=params@ppm,
500 peakwidth=sprintf("%s - %s", params@peakwidth[[1]], params@peakwidth[[2]]),
501 snthresh=params@snthresh,
502 prefilterStep=params@prefilter[[1]],
503 prefilterLevel=params@prefilter[[2]],
504 mzdiff=params@mzdiff,
505 fitgauss=params@fitgauss,
506 noise=params@noise,
507 mzCenterFun=params@mzCenterFun,
508 integrate=params@integrate,
509 firstBaselineCheck=params@firstBaselineCheck,
510 snthreshIsoROIs=!identical(params@roiScales, numeric(0))
511 ))
512 break
513 }
514 }
515 } else {
516 for (list_name in names(process_arg_list)) {
517 param_list <- list()
518 for (param_name in names(process_arg_list[[list_name]])) {
519 param_list[[param_name]] <- process_arg_list[[list_name]][[param_name]]
520 }
521 process_params[[length(process_params)+1]] <- param_list
522 }
523 }
524
499 message("Parameters from previous processes extracted.") 525 message("Parameters from previous processes extracted.")
500 526
501 527
502 indices <- as.numeric(unique(var_meta[, file_grouping_var])) 528 indices <- as.numeric(unique(var_meta[, file_grouping_var]))
503 smol_xcms_set <- orm$smol_xcms_set() 529 smol_xcms_set <- orm$smol_xcms_set()
530 env <- new.env() 556 env <- new.env()
531 ms_file <- xcms::xcmsRaw(sample_path) 557 ms_file <- xcms::xcmsRaw(sample_path)
532 env$tic <- ms_file@tic 558 env$tic <- ms_file@tic
533 env$mz <- ms_file@env$mz 559 env$mz <- ms_file@env$mz
534 env$scanindex <- ms_file@scanindex 560 env$scanindex <- ms_file@scanindex
535 env$scantime <- ms_file@scantime 561 env$scantime <- ms_file@scantime * 60
536 env$intensity <- ms_file@env$intensity 562 env$intensity <- ms_file@env$intensity
537 env$polarity <- as.character(ms_file@polarity[[1]]) 563 env$polarity <- as.character(ms_file@polarity[[1]])
538 564
539 ## Again, ms file is huge, so we get rid of it quickly. 565 ## Again, ms file is huge, so we get rid of it quickly.
540 rm(ms_file) 566 rm(ms_file)
553 } 579 }
554 context$clusters <- list() 580 context$clusters <- list()
555 context$show_percent <- show_percent 581 context$show_percent <- show_percent
556 context$cluster_mean_rt_abundance <- list() 582 context$cluster_mean_rt_abundance <- list()
557 context$central_feature <- list() 583 context$central_feature <- list()
584 context$adducts <- list()
558 load_variable_metadata(orm, var_meta, context) 585 load_variable_metadata(orm, var_meta, context)
559 clusters <- context$clusters 586 clusters <- context$clusters
560 rm(context) 587 rm(context)
561 message("Features enrichment") 588 message("Features enrichment")
562 complete_features(orm, clusters, show_percent) 589 complete_features(orm, clusters, show_percent)
693 if (!is.na(max_o <- extract_peak_var(sample_peak_list, "maxo"))) { 720 if (!is.na(max_o <- extract_peak_var(sample_peak_list, "maxo"))) {
694 dummy_feature$set_max_o(max_o) 721 dummy_feature$set_max_o(max_o)
695 } 722 }
696 } 723 }
697 create_associated_cluster( 724 create_associated_cluster(
725 orm,
698 context$central_feature[[clusterID]], 726 context$central_feature[[clusterID]],
699 dummy_feature, clusterID, 727 dummy_feature, clusterID,
700 context, curent_var_meta, next_pc_group, 728 context, curent_var_meta, next_pc_group,
701 next_align_group 729 next_align_group
702 ) 730 )
759 } 787 }
760 return (clusterID + next_cluster_id) 788 return (clusterID + next_cluster_id)
761 } 789 }
762 790
763 create_associated_cluster <- function( 791 create_associated_cluster <- function(
792 orm,
764 sample_no, feature, clusterID, 793 sample_no, feature, clusterID,
765 context, curent_var_meta, next_pc_group, next_align_group 794 context, curent_var_meta, next_pc_group, next_align_group
766 ) { 795 ) {
767 pcgroup <- as.numeric(curent_var_meta[["pcgroup"]])
768 adduct <- as.character(curent_var_meta[["adduct"]])
769 annotation <- curent_var_meta[["isotopes"]]
770 clusterID <- as.character(clusterID) 796 clusterID <- as.character(clusterID)
771 if (is.null(cluster <- context$clusters[[clusterID]])) { 797 if (is.null(cluster <- context$clusters[[clusterID]])) {
798 pcgroup <- as.numeric(curent_var_meta[["pcgroup"]])
799 adduct_name <- as.character(curent_var_meta[["adduct"]])
800 annotation <- curent_var_meta[["isotopes"]]
772 cluster <- context$clusters[[clusterID]] <- orm$cluster( 801 cluster <- context$clusters[[clusterID]] <- orm$cluster(
773 pc_group=pcgroup + next_pc_group, 802 pc_group=pcgroup + next_pc_group,
774 adduct=adduct, 803 # adduct=adduct,
775 align_group=next_align_group, 804 align_group=next_align_group,
776 # curent_group=curent_group, 805 # curent_group=curent_group,
777 clusterID=context$clusterID, 806 clusterID=context$clusterID,
778 annotation=annotation 807 annotation=annotation
779 ) 808 )
809 if (is.null(adduct <- context$adducts[[adduct_name]])) {
810 context$adducts[[adduct_name]] <- orm$adduct()$load_by(name=adduct_name)$first()
811 if (is.null(adduct <- context$adducts[[adduct_name]])) {
812 adduct <- context$adducts[[adduct_name]] <- orm$adduct(name=adduct_name, charge=0)
813 adduct$save()
814 }
815 }
816 cluster$set_adduct(adduct)
780 ## Crappy hack to assign sample id to cluster without loading the sample. 817 ## Crappy hack to assign sample id to cluster without loading the sample.
781 ## Samples are too big (their sample$env) and slows the process, and eat all the menory 818 ## Samples are too big (their sample$env) and slows the process, and eat all the menory
782 ## so we dont't want to load them. 819 ## so we dont't want to load them.
783 cluster[["sample_id"]] <- context$samples[sample_no][[1]] 820 cluster[["sample_id"]] <- context$samples[sample_no][[1]]
784 cluster$modified__[["sample_id"]] <- cluster[["sample_id"]] 821 cluster$modified__[["sample_id"]] <- cluster[["sample_id"]]