From cba4bac3862c0d231437a2a618ce994d153ab408 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Wed, 26 Jun 2019 12:29:05 +0200
Subject: [PATCH] Add README.org
* README.org: New file.
---
R/mix.R | 47 ++++++++++++++++++++++++++++++++---------------
R/run.R | 4 ++--
man/presc.plot.Rd | 9 +++++++++
3 files changed, 43 insertions(+), 17 deletions(-)
diff --git a/R/mix.R b/R/mix.R
index b4716b5..70e7789 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -470,10 +470,12 @@ presc.p<-function(cl,fn_data,fn_cmpd_l,mode,ppm_lim_fine=10,EIC_limit=0.001) {
##' @param wd Sequence of data dirs containing the prescreen subdir.
##' @param out The name of the output file.
##' @param pal ColorBrewer palette name.
+##' @param cex As in legend.
+##' @param digits Number of significant digits for peak ret times.
##' @return Nothing useful.
##' @author Todor Kondić
##' @export
-presc.plot <- function(wd,out="prescreen.pdf",pal="Dark2") {
+presc.plot <- function(wd,out="prescreen.pdf",pal="Dark2",cex=0.75,digits=6) {
dfdir <- file.path(wd,"prescreen")
pdf(out)
## Get the basenames of eic files.
@@ -493,20 +495,40 @@ presc.plot <- function(wd,out="prescreen.pdf",pal="Dark2") {
dfs <- lapply(dfs,function(x) data.frame(rt=x$rt/60.,intensity=x$intensity))
+ ## Find existing children.
+ maybes <- file.path(dfdir,maybekid)
+ indkids <- which(file.exists(maybes))
+ kids <- maybes[indkids]
+ dfs_kids <- lapply(kids,read.csv,stringsAsFactors=F)
+ dfs_kids <- lapply(dfs_kids,function(x) data.frame(rt=x$retentionTime/60.,intensity= -x$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$intensity[[w]],dfs,w_max)
+ symbs <- LETTERS[1:length(w_max)]
+
+ ## Find max intensities in children
+ w_max_kids <- sapply(dfs_kids,function (x) which.max(abs(x$intensity)))
+ rt_max_kids <- Map(function(df,w) df$rt[[w]],dfs_kids,w_max_kids)
+ i_max_kids <- Map(function(df,w) df$intensity[[w]],dfs_kids,w_max_kids)
+ symbs_kids<- letters[indkids]
rt_rng <- range(sapply(dfs,function(x) x$rt))
- int_rng <- range(sapply(dfs,function(x) x$intensity))
- plot.window(rt_rng,c(int_rng[[1]],1.1*int_rng[[2]]))
+ int_rng <- range(sapply(append(dfs_kids,dfs),function(x) x$intensity))
+ plot.window(rt_rng,c(1.2*int_rng[[1]],1.3*int_rng[[2]]))
box()
cols <- RColorBrewer::brewer.pal(n=length(dfs),name=pal)
- legend("top",horiz=T,legend=lbls,col=cols,fill=cols)
+ lgnd <- Map(function(k,v) paste(k,"= ",v,sep=''),symbs,format(rt_max,digits=digits))
+ linfo <- legend("topleft",horiz=T,legend=lbls,col=cols,fill=cols,bty="n",cex=cex)
+ legend(x=linfo$rect$left,y=linfo$rect$top-0.5*linfo$rect$h,horiz=T,legend=lgnd,fill=cols,bty="n",cex=cex)
+
+ cols_kids <- cols[indkids]
+ lgnd_kids <- Map(function(k,v) paste(k,"= ",v,sep=''),symbs_kids,format(rt_max_kids,digits=digits))
+ if (length(lgnd_kids)>0) legend(x="bottomleft",horiz=T,legend=lgnd_kids,fill=cols[indkids],bty="n",cex=cex)
## Plot eic across the directory set.
for (n in seq(length(dfs))) {
@@ -515,19 +537,14 @@ presc.plot <- function(wd,out="prescreen.pdf",pal="Dark2") {
lines(df$intensity ~ df$rt,col=col)
}
- ## 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,read.csv,stringsAsFactors=F)
- for (df in dfs) {
- lines(intensity ~ retentionTime,data=df,type="h",col="black")
+ if (length(dfs_kids) >0) {
+ for (k in 1:length(indkids)) {
+ lines(intensity ~ rt,data=dfs_kids[[k]],type="h",col=cols_kids[[k]])
+ }
}
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)
+ for (k in seq(length(w_max))) text(rt_max[[k]],i_max[[k]],labels=symbs[[k]],pos=4,offset=0.5*k)
+ if (length(dfs_kids)>0) for (k in seq(length(w_max_kids))) text(rt_max_kids[[k]],i_max_kids[[k]],labels=symbs_kids[[k]],pos=4,offset=0.5*k)
axis(1)
axis(2)
gc()
diff --git a/R/run.R b/R/run.R
index fbc3c2f..b4187cc 100644
--- a/R/run.R
+++ b/R/run.R
@@ -68,7 +68,7 @@ sw.do<-function(fn_data,fn_cmpd_list,mode,rdir=".",combine=F,proc=F) {
stgs<-sapply(basename(wdirs),function (nm) paste(nm,"yml",sep='.'))
if (proc) {
- cl<-parallel::makeCluster(proc)
+ cl<-parallel::makeCluster(proc,type='FORK')
p.sw(fn_data,stgs,wdirs,fn_cmpd_list,mode,combine=combine,cl=cl)
} else {
v(fn_data,stgs,wdirs,fn_cmpd_list,mode,combine=combine)
@@ -116,7 +116,7 @@ mb.do<-function(mb,rdir=".",proc=F) {
fn_stgs<-sapply(names(mb),function(n) file.path(idir(n),attch(n,'.ini')))
if (proc) {
- cl<-parallel::makeCluster(proc)
+ cl<-parallel::makeCluster(proc,type='FORK')
mb.p(mb,infodir,fn <- stgs,cl=cl)
} else {
mb.v(mb,infodir,fn_stgs)
diff --git a/man/presc.plot.Rd b/man/presc.plot.Rd
index 4630dd7..b6721d1 100644
--- a/man/presc.plot.Rd
+++ b/man/presc.plot.Rd
@@ -4,7 +4,11 @@
\alias{presc.plot}
\title{Plot the Output of Prescreen}
\usage{
+presc.plot(wd, out = "prescreen.pdf", pal = "Dark2", cex = 0.75,
+ digits = 6)
+
presc.plot(wd, out = "prescreen.pdf", pal = "Accent")
+
}
\arguments{
\item{wd}{Sequence of data dirs containing the prescreen subdir.}
@@ -12,6 +16,11 @@ presc.plot(wd, out = "prescreen.pdf", pal = "Accent")
\item{out}{The name of the output file.}
\item{pal}{ColorBrewer palette name.}
+
+
+\item{cex}{As in legend.}
+
+\item{digits}{Number of significant digits for peak ret times.}
}
\value{
Nothing useful.
--
GitLab