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Added my_plotEICs.R function. It implements a bug fix that addresses …
…an error found in the color labels of CAMERA's plotEICs plots.
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| # We are currently receiving an error when running ParseCAMERA with gen.plots = TRUE | ||
| #Munge Data Modules | ||
| #if positive, run: | ||
| # ParseCAMERA(from.table = "Annotated", to.table = "output_parsed", CAMERA.obj = "anposGa") | ||
| # | ||
| # Error in .local(object, ...) : | ||
| # xcmsSource: file not found: E:\ORD Backup\Users\jmosley\Desktop\WLSSD 2014 Livers\mzML/Pooled QCs/Pooled_QC_Pos_10.mzML | ||
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| #To get around this, set the variables in the script below and run *AFTER* running the InitWorkflow() module. Then execute the remaining script code to bypass the bug. | ||
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| ##Set these variables to be equivalent on your local system | ||
| data_dir <- "O:/Public/jmosl01/LUMA-Data" | ||
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| ##Execute this code only after setting the above variables for your local system | ||
| new_filepaths <- list.files(path = data_dir, recursive = TRUE, full.names = TRUE) | ||
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| if(BLANK) new_filepaths <- new_filepaths[grepl("Blanks", new_filepaths)] | ||
| if(!BLANK) new_filepaths <- new_filepaths[!grepl("Blanks", new_filepaths)] | ||
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| #If Positive mode, run this: | ||
| new_filepaths <- new_filepaths[grepl(ion.id[1],new_filepaths)] | ||
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| anposGa@xcmsSet@filepaths <- new_filepaths | ||
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| #If Negative mode, run this: | ||
| new_filepaths <- new_filepaths[grepl(ion.id[2],new_filepaths)] | ||
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| annegGa@xcmsSet@filepaths <- new_filepaths |
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| # | ||
| # This function is a modified version of CAMERA's plotEICs. It implements a bug fix that | ||
| # addresses an error with the color labels in the plots. Bug fix was first proposed by | ||
| # Jonathan Mosley. | ||
| # | ||
| my_plotEICs <- function (object, pspec = 1:length(object@pspectra), maxlabel = 0, | ||
| sleep = 0, method = "bin") | ||
| { | ||
| smpls <- unique(object@psSamples[pspec]) | ||
| xeic <- new("xcmsEIC") | ||
| xeic@rtrange <- matrix(nrow = length(pspec), ncol = 2) | ||
| xeic@mzrange <- matrix(nrow = length(pspec), ncol = 2) | ||
| pcpos <- 1 | ||
| rtmargin <- 1 | ||
| for (a in seq(along = smpls)) { | ||
| xraw <- xcmsRaw(object@xcmsSet@filepaths[smpls[a]], | ||
| profmethod = method) | ||
| pspecS <- pspec[which(object@psSamples[pspec] == smpls[a])] | ||
| peaks <- CAMERA:::getPeaks(object@xcmsSet, smpls[a]) | ||
| eic <- lapply(pspecS, function(pc) { | ||
| pidx <- object@pspectra[[pc]] | ||
| pks <- peaks[pidx, , drop = FALSE] | ||
| gks <- object@groupInfo[pidx, , drop = FALSE] | ||
| nap <- which(is.na(pks[, 1])) | ||
| pks[nap, ] <- cbind(gks[nap, c(1:6), drop = FALSE], | ||
| matrix(nrow = length(nap), ncol = 5, 0)) | ||
| bbox <- c(rtmin = min(pks[, "rtmin"]) - rtmargin, | ||
| rtmax = max(pks[, "rtmax"]) + rtmargin, | ||
| mzmin = min(pks[,"mzmin"]), | ||
| mzmax = max(pks[, "mzmax"])) | ||
| eic <- xcms:::getEIC(xraw, rtrange = pks[, c("rtmin","rtmax"), drop = FALSE], | ||
| mzrange = pks[, c("mzmin","mzmax"), drop = FALSE]) | ||
| xeic@rtrange[pcpos, ] <<- bbox[c("rtmin", "rtmax")] | ||
| xeic@mzrange[pcpos, ] <<- bbox[c("mzmin", "mzmax")] | ||
| cat("-->", pcpos, "\n") | ||
| pcpos <<- pcpos + 1 | ||
| eic@eic[[1]] | ||
| }) | ||
| xeic@eic <- c(xeic@eic, eic) | ||
| } | ||
| names(xeic@eic) <- paste("Pseudospectrum ", pspec, sep = "") | ||
| if (maxlabel > 0) { | ||
| col <- rainbow(maxlabel) | ||
| } | ||
| else { | ||
| col <- c() | ||
| } | ||
| for (ps in seq(along = pspec)) { | ||
| EIC <- xeic@eic[[ps]] | ||
| pidx <- object@pspectra[[pspec[ps]]] | ||
| peaks <- CAMERA:::getPeaks(object@xcmsSet, object@psSamples[pspec[ps]])[pidx,, drop = FALSE] | ||
| grps <- object@groupInfo[pidx, ] | ||
| nap <- which(is.na(peaks[, 1])) | ||
| naps <- rep(FALSE, nrow(peaks)) | ||
| if (length(nap) > 0) { | ||
| naps[nap] <- TRUE | ||
| peaks[nap, ] <- cbind(grps[nap, c(1:6), drop = FALSE], | ||
| matrix(nrow = length(nap), ncol = 5, 0)) | ||
| } | ||
| main <- paste("Pseudospectrum ", pspec[ps], sep = "") | ||
| neics <- length(pidx) | ||
| lmaxlabel <- min(maxlabel, neics) | ||
| eicidx <- 1:neics | ||
| maxint <- numeric(length(eicidx)) | ||
| for (j in eicidx) { | ||
| maxint[j] <- max(EIC[[j]][, "intensity"]) | ||
| } | ||
| o <- order(maxint, decreasing = TRUE) | ||
| rt <- xeic@rtrange[ps, ] | ||
| rt.min <- round(mean(peaks[, "rtmin"]), digits = 3) | ||
| rt.med <- round(peaks[o[1], "rt"], digits = 3) | ||
| rt.max <- round(mean(peaks[, "rtmax"]), digits = 3) | ||
| plot(0, 0, type = "n", xlim = rt, ylim = c(0, max(maxint)), | ||
| xaxs = "i", xlab = "Retention Time (seconds)", | ||
| ylab = "Intensity", main = paste("Extracted Ion Chromatograms for ", | ||
| main, "\nTime: From", rt.min, "to", rt.max, | ||
| ", mean", rt.med)) | ||
| lcol <- rgb(0.6, 0.6, 0.6) | ||
| lcol <- c(col, rep(lcol, max(nrow(peaks) - maxlabel,0))) | ||
| cnt <- 1 | ||
| for (j in eicidx[o]) { | ||
| pts <- xeic@eic[[ps]][[j]] | ||
| points(pts, type = "l", col = lcol[cnt]) | ||
| peakrange <- peaks[, c("rtmin", "rtmax"), drop = FALSE] | ||
| ptsidx <- pts[, "rt"] >= peakrange[j, 1] & pts[,"rt"] <= peakrange[j, 2] | ||
| if (naps[j]) { | ||
| points(pts[ptsidx, ], type = "l", col = col[cnt],lwd = 1.3, lty = 3) | ||
| } | ||
| else { | ||
| points(pts[ptsidx, ], type = "l", col = col[cnt],lwd = 1.3) | ||
| } | ||
| cnt <- cnt + 1 | ||
| } | ||
| pspectrum <- getpspectra(object, grp = pspec[ps]) | ||
| mz <- pspectrum[o, "mz"] | ||
| if (lmaxlabel > 0 & "adduct" %in% colnames(pspectrum)) { | ||
| adduct <- sub("^ ", "", pspectrum[o, "adduct"]) | ||
| mass <- sapply(strsplit(adduct, " "), function(x) { | ||
| x[2] | ||
| }) | ||
| adduct <- sapply(strsplit(adduct, " "), function(x) { | ||
| x[1] | ||
| }) | ||
| umass <- unique(na.omit(mass[1:maxlabel])) | ||
| adduct[is.na(adduct)] <- "" | ||
| test <- vector("list", length = length(mz)) | ||
| mz <- format(pspectrum[o[1:lmaxlabel], "mz"], | ||
| digits = 5) | ||
| if (length(umass) > 0) { | ||
| for (i in 1:length(umass)) { | ||
| ini <- which(mass == umass[i]) | ||
| for (ii in 1:length(ini)) { | ||
| firstpart <- strsplit(adduct[ini[ii]],"M")[[1]][1] | ||
| secondpart <- strsplit(adduct[ini[ii]],"M")[[1]][2] | ||
| masspart <- mz[ini[ii]] | ||
| test[[ini[ii]]] <- substitute(paste(masspart," ", firstpart, M[i], secondpart), | ||
| list(firstpart = firstpart, | ||
| i = i, | ||
| secondpart = secondpart, | ||
| masspart = masspart)) | ||
| } | ||
| } | ||
| } | ||
| for (i in seq(along = lmaxlabel)) { | ||
| if (is.null(test[[i]])) { | ||
| test[[i]] <- mz[i] | ||
| } | ||
| } | ||
| leg <- as.expression(test[1:lmaxlabel]) | ||
| legend("topright", legend = leg, col = lcol,lty = 1) | ||
| } | ||
| if (sleep > 0) { | ||
| Sys.sleep(sleep) | ||
| } | ||
| } | ||
| } |
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Hi Wilson,
I am going to rollback any code changes related to the my_plotEICs.R function, effectively doing away with the addition of this custom CAMERA function to LUMA. Instead, I will submit a bug fix to CAMERA for the known issue in CAMERA "Bug in labelling and/or legend of plotEICs" (sneumann/CAMERA#2)
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Hi Jonathan,
Sounds good. Thanks for the update.
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Hi Wilson,
I finished the bug fix and submitted a pull request to @sneumann: sneumann/CAMERA#55 to fix sneumann/CAMERA#2.
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Hi Jonathan,
That's great to know. Let's hope @sneumann is more responsive this time around. Thanks for the update.