Mercurial > repos > computational-metabolomics > mspurity_combineannotations
view averageFragSpectra.R @ 1:cf62d2c0104e draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
author | computational-metabolomics |
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date | Thu, 05 Dec 2019 07:47:31 -0500 |
parents | 7f3183988100 |
children | 18c0038dde9c |
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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$method <- 'all' } combined <- plyr::rbind.fill(av_intra_df, av_inter_df, av_all_df) return(combined) } option_list <- list( make_option("--out_rdata", type="character"), make_option("--out_peaklist", type="character"), make_option("--pa", type="character"), make_option("--av_level", type="character"), make_option("--minfrac", default=0.5), make_option("--minnum", default=1), make_option("--ppm", default=5.0), make_option("--snr", default=0), make_option("--ra", default=0), make_option("--av", default="median", type="character"), make_option("--sumi", action="store_true"), make_option("--rmp", action="store_true"), make_option("--cores", default=1) ) opt <- parse_args(OptionParser(option_list=option_list)) print(opt) loadRData <- function(rdata_path, name){ #loads an RData file, and returns the named xset object if it is there load(rdata_path) return(get(ls()[ls() %in% name])) } # Requires pa <- loadRData(opt$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$avid <- 1:nrow(av_spectra) filenames <- sapply(av_spectra$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') } }