Mercurial > repos > computational-metabolomics > mspurity_filterfragspectra
view averageFragSpectra.R @ 7:2e10c13085c9 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
author | computational-metabolomics |
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date | Tue, 08 Feb 2022 14:02:03 +0000 |
parents | cc0f8ddad4a8 |
children | a46824d13914 |
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library(optparse) library(msPurity) library(xcms) print(sessionInfo()) get_av_spectra <- function(x) { if (length(x$av_intra) > 0) { av_intra_df <- plyr::ldply(x$av_intra) if (nrow(av_intra_df) == 0) { av_intra_df <- NULL }else{ av_intra_df$method <- "intra" } }else{ av_intra_df <- NULL } if ((is.null(x$av_inter)) || (nrow(x$av_inter) == 0)) { av_inter_df <- NULL }else{ av_inter_df <- x$av_inter av_inter_df$method <- "inter" } if ((is.null(x$av_all)) || (nrow(x$av_all) == 0)) { av_all_df <- NULL }else{ av_all_df <- x$av_all av_all_df$method <- "all" } combined <- plyr::rbind.fill(av_intra_df, av_inter_df, av_all_df) return(combined) } option_list <- list( make_option("--out_rdata", type = "character"), make_option("--out_peaklist", type = "character"), make_option("--pa", type = "character"), make_option("--av_level", type = "character"), make_option("--minfrac", default = 0.5), make_option("--minnum", default = 1), make_option("--ppm", default = 5.0), make_option("--snr", default = 0), make_option("--ra", default = 0), make_option("--av", default = "median", type = "character"), make_option("--sumi", action = "store_true"), make_option("--rmp", action = "store_true"), make_option("--cores", default = 1) ) opt <- parse_args(OptionParser(option_list = option_list)) print(opt) load_r_data <- function(rdata_path, name) { #loads an RData file, and returns the named xset object if it is there load(rdata_path) return(get(ls()[ls() %in% name])) } # Requires pa <- load_r_data(opt$pa, "pa") pa@cores <- opt$cores if (is.null(opt$rmp)) { rmp <- FALSE }else{ rmp <- TRUE } if (is.null(opt$sumi)) { sumi <- FALSE }else{ sumi <- TRUE } if (opt$av_level == "intra") { pa <- msPurity::averageIntraFragSpectra(pa, minfrac = opt$minfrac, minnum = opt$minnum, ppm = opt$ppm, snr = opt$snr, ra = opt$ra, av = opt$av, sumi = sumi, rmp = rmp, cores = opt$cores) } else if (opt$av_level == "inter") { pa <- msPurity::averageInterFragSpectra(pa, minfrac = opt$minfrac, minnum = opt$minnum, ppm = opt$ppm, snr = opt$snr, ra = opt$ra, av = opt$av, sumi = sumi, rmp = rmp, cores = opt$cores) } else if (opt$av_level == "all") { pa <- msPurity::averageAllFragSpectra(pa, minfrac = opt$minfrac, minnum = opt$minnum, ppm = opt$ppm, snr = opt$snr, ra = opt$ra, av = opt$av, sumi = sumi, rmp = rmp, cores = opt$cores) } print(pa) save(pa, file = opt$out_rdata) if (length(pa) > 0) { av_spectra <- plyr::ldply(pa@av_spectra, get_av_spectra) if (nrow(av_spectra) == 0) { message("No average spectra available") } else { colnames(av_spectra)[1] <- "grpid" av_spectra$grpid <- names(pa@av_spectra)[av_spectra$grpid] if ((length(pa@av_intra_params) > 0) || (length(pa@av_inter_params) > 0)) { # Add some extra info (only required if av_intra or av_inter performed) colnames(av_spectra)[2] <- "fileid" av_spectra$avid <- seq_len(nrow(av_spectra)) filenames <- sapply(av_spectra$fileid, function(x) names(pa@fileList)[as.integer(x)]) # filenames_galaxy <- sapply( # av_spectra$fileid, function(x) basename(pa@fileList[as.integer(x)])) av_spectra <- as.data.frame( append(av_spectra, list(filename = filenames), after = 2)) } print(head(av_spectra)) write.table(av_spectra, opt$out_peaklist, row.names = FALSE, sep = "\t") } }