Mercurial > repos > computational-metabolomics > mspurity_purityx
view purityX.R @ 11:d84cc9960035 draft default tip
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 94f746247c464fb270358421399810d8a9fb9e8a
author | computational-metabolomics |
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date | Fri, 13 Sep 2024 13:36:43 +0000 |
parents | 13034c3886f2 |
children |
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library(msPurity) library(optparse) print(sessionInfo()) option_list <- list( make_option(c("--xset_path"), type = "character"), make_option(c("-o", "--out_dir"), type = "character"), make_option(c("--mzML_path"), type = "character"), make_option("--minOffset", default = 0.5), make_option("--maxOffset", default = 0.5), make_option("--ilim", default = 0.05), make_option("--iwNorm", default = "none", type = "character"), make_option("--exclude_isotopes", action = "store_true"), make_option("--isotope_matrix", type = "character"), make_option("--purityType", default = "purityFWHMmedian"), make_option("--singleFile", default = 0), make_option("--cores", default = 4), make_option("--xgroups", type = "character"), make_option("--camera_xcms", default = "xset"), make_option("--files", type = "character"), make_option("--galaxy_files", type = "character"), make_option("--choose_class", type = "character"), make_option("--ignore_files", type = "character"), make_option("--rtraw_columns", action = "store_true") ) opt <- parse_args(OptionParser(option_list = option_list)) print(opt) if (!is.null(opt$xgroups)) { xgroups <- as.numeric(strsplit(opt$xgroups, ",")[[1]]) } else { xgroups <- NULL } print(xgroups) if (!is.null(opt$remove_nas)) { df <- df[!is.na(df$mz), ] } if (is.null(opt$isotope_matrix)) { im <- NULL } else { im <- read.table(opt$isotope_matrix, header = TRUE, sep = "\t", stringsAsFactors = FALSE ) } if (is.null(opt$exclude_isotopes)) { isotopes <- FALSE } else { isotopes <- TRUE } if (is.null(opt$rtraw_columns)) { rtraw_columns <- FALSE } else { rtraw_columns <- TRUE } loadRData <- function(rdata_path, xnames) { # loads an RData file, and returns the named xset object if it is there load(rdata_path) return(get(ls()[ls() %in% xnames])) } getxcmsSetObject <- function(xobject) { # XCMS 1.x if (class(xobject) == "xcmsSet"){ return(xobject) } # XCMS 3.x if (class(xobject) == "XCMSnExp") { # Get the legacy xcmsSet object suppressWarnings(xset <- as(xobject, "xcmsSet")) if (!is.null(xset@phenoData$sample_group)){ xcms::sampclass(xset) <- xset@phenoData$sample_group }else{ xcms::sampclass(xset) <- "." } return(xset) } } target_obj <- loadRData(opt$xset_path, c('xset', 'xa', 'xdata')) if (opt$camera_xcms == "camera") { xset <- target_obj@xcmsSet } else { xset <- target_obj } xset <- getxcmsSetObject(xset) print(xset) minOffset <- as.numeric(opt$minOffset) maxOffset <- as.numeric(opt$maxOffset) if (opt$iwNorm == "none") { iwNorm <- FALSE iwNormFun <- NULL } else if (opt$iwNorm == "gauss") { iwNorm <- TRUE iwNormFun <- msPurity::iwNormGauss(minOff = -minOffset, maxOff = maxOffset) } else if (opt$iwNorm == "rcosine") { iwNorm <- TRUE iwNormFun <- msPurity::iwNormRcosine(minOff = -minOffset, maxOff = maxOffset) } else if (opt$iwNorm == "QE5") { iwNorm <- TRUE iwNormFun <- msPurity::iwNormQE.5() } print(xset@filepaths) if (!is.null(opt$files)) { updated_filepaths <- trimws(strsplit(opt$files, ",")[[1]]) updated_filepaths <- updated_filepaths[updated_filepaths != ""] print(updated_filepaths) updated_filenames <- basename(updated_filepaths) original_filenames <- basename(xset@filepaths) update_idx <- match(updated_filenames, original_filenames) if (!is.null(opt$galaxy_files)) { galaxy_files <- trimws(strsplit(opt$galaxy_files, ",")[[1]]) galaxy_files <- galaxy_files[galaxy_files != ""] xset@filepaths <- galaxy_files[update_idx] } else { xset@filepaths <- updated_filepaths[update_idx] } } if (!is.null(opt$choose_class)) { classes <- trimws(strsplit(opt$choose_class, ",")[[1]]) ignore_files_class <- which(!as.character(xset@phenoData$class) %in% classes) print("choose class") print(ignore_files_class) } else { ignore_files_class <- NA } if (!is.null(opt$ignore_files)) { ignore_files_string <- trimws(strsplit(opt$ignore_files, ",")[[1]]) filenames <- rownames(xset@phenoData) ignore_files <- which(filenames %in% ignore_files_string) ignore_files <- unique(c(ignore_files, ignore_files_class)) ignore_files <- ignore_files[ignore_files != ""] } else { if (anyNA(ignore_files_class)) { ignore_files <- NULL } else { ignore_files <- ignore_files_class } } print("ignore_files") print(ignore_files) ppLCMS <- msPurity::purityX( xset = xset, offsets = c(minOffset, maxOffset), cores = opt$cores, xgroups = xgroups, purityType = opt$purityType, ilim = opt$ilim, isotopes = isotopes, im = im, iwNorm = iwNorm, iwNormFun = iwNormFun, singleFile = opt$singleFile, fileignore = ignore_files, rtrawColumns = rtraw_columns ) dfp <- ppLCMS@predictions # to make compatable with deconrank # (keep grpid for other compatibility) dfp <- data.frame("peakID"=dfp$grpid, dfp) colnames(dfp)[colnames(dfp) == "median"] <- "medianPurity" colnames(dfp)[colnames(dfp) == "mean"] <- "meanPurity" colnames(dfp)[colnames(dfp) == "sd"] <- "sdPurity" colnames(dfp)[colnames(dfp) == "stde"] <- "sdePurity" colnames(dfp)[colnames(dfp) == "RSD"] <- "cvPurity" colnames(dfp)[colnames(dfp) == "pknm"] <- "pknmPurity" if (sum(is.na(dfp$medianPurity)) > 0) { dfp[is.na(dfp$medianPurity), ]$medianPurity <- 0 } print(head(dfp)) write.table(dfp, file.path(opt$out_dir, "purityX_output.tsv"), row.names = FALSE, sep = "\t") save.image(file.path(opt$out_dir, "purityX_output.RData"))