Update mix.R and run.R

Finally plotting works nicely.

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()

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)