diff --git a/R/mix.R b/R/mix.R
index 7df790f6098ef5c5a725d20d1b9b7b07bcab312d..b4716b55c605db75e9923d6ec74cefaa604007f5 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -354,80 +354,6 @@ v<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir="ar
}
}
-
-##' Prescreens. Ripped off from ReSOLUTION
-##'
-##'
-##' @title Prescreen
-##' @param archive_name ...
-##' @param RMB_mode ...
-##' @param FileList ...
-##' @param cmpd_list ...
-##' @param ppm_limit_fine ...
-##' @param EIC_limit ...
-##' @author Emma Schymanski, Todor Kondić
-RMB_EIC_prescreen_intrn <- function (archive_name, RMB_mode, FileList, cmpd_list,
- ppm_limit_fine = 10, EIC_limit = 0.001) {
- pdf_title <- paste(archive_name, "_EICscan.pdf", sep = "")
- pdf(pdf_title)
- n_spec <- 0
- cmpd_RT_maxI <- ""
- msms_found <- ""
- rts <- 0
- max_I_prec <- ""
- cmpd_RT_maxI_min <- ""
- file_list <- read.csv(FileList, stringsAsFactors = FALSE)
- cmpd_info <- read.csv(cmpd_list, stringsAsFactors = FALSE)
- f <- mzR::openMSfile(file_list$Files[1])
- for (i in 1:length(file_list$ID)) {
- cpdID <- file_list$ID[i]
- n_spec <- n_spec + 1
- smiles <- tryCatch(RMassBank::findSmiles(cpdID), error = function(e) NA)
- if (!is.na(smiles)) {
- mz <- as.numeric(RMassBank::findMz(cpdID, RMB_mode)[3])
- }
- else {
- mz <- as.numeric(RMassBank::findMz(cpdID, RMB_mode, retrieval = "unknown")[3])
- }
- eic <- RMassBank::findEIC(f, mz, limit = EIC_limit)
- msms_found[n_spec] <- FALSE
- msms <- RMassBank::findMsMsHR.mass(f, mz, 0.5, RMassBank::ppm(mz, ppm_limit_fine,
- p = TRUE))
- max_I_prec_index <- which.max(eic$intensity)
- cmpd_RT_maxI[n_spec] <- eic[max_I_prec_index, 1]
- max_I_prec[n_spec] <- eic[max_I_prec_index, 2]
- cmpd_RT_maxI_min[n_spec] <- as.numeric(cmpd_RT_maxI[n_spec])/60
- plot.new()
- plot.window(range(eic$rt), range(eic$intensity))
- box()
- lines(eic$intensity ~ eic$rt)
- for (specs in msms) {
- if (specs@found == TRUE) {
- df <- do.call(rbind, lapply(specs@children, function(sp) c(sp@rt,
- intensity = max(sp@intensity))))
- lines(intensity ~ retentionTime, data = df, type = "h",
- col = "blue")
- msms_found[n_spec] <- TRUE
- }
- }
- title(main = cpdID, xlab = "RT (sec)", ylab = "Intensity")
- text(as.numeric(cmpd_RT_maxI[n_spec]), as.numeric(max_I_prec[n_spec]),
- labels = as.numeric(cmpd_RT_maxI_min[n_spec]), pos = 4)
- axis(1)
- axis(2)
- gc()
- rts[i] <- (cmpd_RT_maxI[n_spec])
- }
- dev.off()
- write.csv(cbind(file_list$ID, cmpd_info$mz, cmpd_info$Name,
- cmpd_RT_maxI, cmpd_RT_maxI_min, max_I_prec, msms_found),
- file = paste(archive_name, "_RTs_wI.csv", sep = ""),
- row.names = F)
-}
-
-
-
-
##' Prescreens. Writes data out. Adapted from ReSOLUTION
##'
##'
@@ -547,7 +473,7 @@ presc.p<-function(cl,fn_data,fn_cmpd_l,mode,ppm_lim_fine=10,EIC_limit=0.001) {
##' @return Nothing useful.
##' @author Todor Kondić
##' @export
-presc.plot <- function(wd,out="prescreen.pdf",pal="Accent") {
+presc.plot <- function(wd,out="prescreen.pdf",pal="Dark2") {
dfdir <- file.path(wd,"prescreen")
pdf(out)
## Get the basenames of eic files.
@@ -556,26 +482,32 @@ presc.plot <- function(wd,out="prescreen.pdf",pal="Accent") {
for (i in seq(length(eics))) {
eic <- eics[[i]]
maybekid <- maybekids[[i]]
+ fn_ini <- lapply(wd,function(x) file.path(x,list.files(path=x,patt="*.ini")[[1]]))
+
+ lbls <- lapply(fn_ini,function(x) {s <- yaml::yaml.load_file(x);s$spectraList[[1]]$ce})
plot.new()
dfs <- lapply(file.path(dfdir,eic),function(fn) {
tryCatch(read.csv(fn,stringsAsFactors = F),
error=function(e) {message(paste(e,"; offending file:",fn))})
})
+
+ dfs <- lapply(dfs,function(x) data.frame(rt=x$rt/60.,intensity=x$intensity))
+ ## Find max intensities.
+ w_max <- sapply(dfs,function (x) which.max(x$intensity))
+ rt_max <- Map(function(df,w) df$rt[[w]],dfs,w_max)
+ i_max<- Map(function(df,w) df$intensity[[w]],dfs,w_max)
- ## Find max intensity for the first in the group.
- imx <- which.max(dfs[[1]]$intensity)
- int_max <- dfs[[1]]$intensity[[imx]]
- rt_max <- dfs[[1]]$rt[[imx]]
- rt_min_max <- as.numeric(rt_max)/60.
rt_rng <- range(sapply(dfs,function(x) x$rt))
int_rng <- range(sapply(dfs,function(x) x$intensity))
- plot.window(rt_rng,int_rng)
+ plot.window(rt_rng,c(int_rng[[1]],1.1*int_rng[[2]]))
box()
cols <- RColorBrewer::brewer.pal(n=length(dfs),name=pal)
+ legend("top",horiz=T,legend=lbls,col=cols,fill=cols)
+
## Plot eic across the directory set.
for (n in seq(length(dfs))) {
df <- dfs[[n]]
@@ -585,21 +517,17 @@ presc.plot <- function(wd,out="prescreen.pdf",pal="Accent") {
## Find existing children and plot them across the directory
## set.
+
maybes <- file.path(dfdir,maybekid)
indkids <- which(file.exists(maybes))
kids <- maybes[indkids]
- dfs <- lapply(kids,function(fn) {
- tryCatch(read.csv(fn,stringsAsFactors=F),
- error=function(e) {message(paste(e,"; offending file:",fn))
- return(NA)},
- finally={return(NA)})
- })
- dfs <- dfs[!is.na(dfs)]
+
+ dfs <- lapply(kids,read.csv,stringsAsFactors=F)
for (df in dfs) {
- lines(intensity~retentionTime,data=df,type="h",col="blue")
+ lines(intensity ~ retentionTime,data=df,type="h",col="black")
}
- title(main=i,xlab="retention time [s]",ylab="intensity")
- text(as.numeric(rt_max),as.numeric(int_max),labels=as.numeric(rt_min_max),pos=4)
+ title(main=i,xlab="retention time [min]",ylab="intensity")
+ for (i in seq(length(w_max))) text(rt_max[[i]],i_max[[i]],labels=rt_max[[i]],pos=4)
axis(1)
axis(2)
gc()
diff --git a/R/run.R b/R/run.R
index e5d36dad7856e3141acab770507d3d64671f42ee..fbc3c2f96680decbd27501b25a932869c6664b14 100644
--- a/R/run.R
+++ b/R/run.R
@@ -23,7 +23,7 @@ presc.do<-function(fn_data,fn_cmpd_list,mode,proc=F) {
if (proc) {
- cl<-parallel::makeCluster(proc)
+ cl<-parallel::makeCluster(proc,type='FORK')
presc.p(cl=cl,fn_data,fn_cmpd_l=fn_cmpd_list,mode=mode)
} else {
presc.v(fn_data,fn_cmpd_l=fn_cmpd_list,mode)