From c8328a12b237a55e6f1dba9e4aff0f91987fd740 Mon Sep 17 00:00:00 2001
From: Mira Narayanan <mira.narayanan@ext.uni.lu>
Date: Thu, 11 Jul 2019 15:47:53 +0200
Subject: [PATCH] Reorganise prescreening plots using layout structure.
---
R/mix.R | 46 ++++++++++++++++++++++------------------------
1 file changed, 22 insertions(+), 24 deletions(-)
diff --git a/R/mix.R b/R/mix.R
index ae0be4b..bdf7960 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -380,7 +380,6 @@ presc.plot <- function(wd,mode,out="prescreen.pdf",pal="Dark2",cex=0.75,rt_digit
blahnh4="MpNH4_mass",
blahna="MpNa_mass")
dfdir <- file.path(wd,"prescreen")
- pdf(out)
wd1 <- wd[[1]]
df <- read.csv(file=get_cmpd_l_fn(wd1),stringsAsFactors = F)
@@ -398,8 +397,9 @@ presc.plot <- function(wd,mode,out="prescreen.pdf",pal="Dark2",cex=0.75,rt_digit
## Get the basenames of eic files.
eics <- list.files(path=dfdir[[1]],patt=".*eic.csv")
maybekids <- sapply(strsplit(eics,split="\\."),function(x) {paste(x[[1]][1],'.kids.csv',sep='')})
+
+ pdf(out)
for (i in seq(length(eics))) {
- plot.new()
eic <- eics[[i]]
maybekid <- maybekids[[i]]
fn_ini <- lapply(wd,get_stgs_fn)
@@ -434,33 +434,30 @@ presc.plot <- function(wd,mode,out="prescreen.pdf",pal="Dark2",cex=0.75,rt_digit
- rt_rng <- 1.2*range(sapply(dfs,function(x) x$rt))
- int_rng <- 1.4*range(sapply(append(dfs_kids,dfs),function(x) x$intensity))
- plot.window(rt_rng,int_rng)
- box()
+ rt_rng <- range(sapply(dfs,function(x) x$rt))
+ int_rng <- range(sapply(append(dfs_kids,dfs),function(x) x$intensity))
cols <- RColorBrewer::brewer.pal(n=length(dfs),name=pal)
lgnd <- Map(function(k,v) paste(k,"= ",formatC(v,format="f",digits=rt_digits),sep=''),symbs,rt_max)
+
+ layout(matrix(c(1,2,3,3), 2, 2, byrow = TRUE),
+ widths=c(7,8), heights=c(6,6))
+ struc_xr <- c(0,100)
+ struc_yr <- c(0,100)
+ plot(1,1,type="n",xlab="",ylab="",xlim=struc_xr,ylim=struc_yr,xaxt="n",yaxt="n")
+ rendersmiles2(osmesi[i],coords=c(struc_xr[1],struc_yr[1],struc_xr[2],struc_yr[2]))
+
+ col_eng <- c(0,100)
+ peak_int <- c(0,100)
+ plot(1,1,type="n",xlab="",ylab="",xlim=col_eng,ylim=peak_int,xaxt="n",yaxt="n",axes = FALSE)
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)
- #text(x=rt_rng[[2]],y=0.5*int_rng[[2]],osmesi[[i]],cex=cex,srt=90)
- fxmin=rt_rng[1]+0.75*(rt_rng[2]-rt_rng[1])
- fxmax=fxmin+0.3*(rt_rng[2]-rt_rng[1])
- fymin=int_rng[1]+0.6*(int_rng[2]-int_rng[1])
- fymax=fymin+0.3*(int_rng[2]-int_rng[1])
-
- xcmp=c(fxmin,fxmax)
- ycmp=c(fymin,fymax)
- #xcmp=c(0.99*rt_rng[[1]],rt_rng[[2]])
-
- #ycmp=c(0.99*int_rng[[1]],int_rng[[2]])
- rendersmiles2(osmesi[i],coords=c(xcmp[1],ycmp[1],xcmp[2],ycmp[2]))
- # RChemMass::renderSMILES.rcdk(osmesi[i],coords=c(xcmp[[1]],ycmp[[1]],xcmp[[2]],ycmp[[2]]),width=xcmp[[2]]-xcmp[[1]],height=ycmp[[2]]-ycmp[[1]])
-
+ 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,"= ",formatC(v,digits=rt_digits,format="f"),sep=''),symbs_kids,rt_max_kids)
- if (length(lgnd_kids)>0) legend(x="bottomleft",horiz=T,legend=lgnd_kids,fill=cols[indkids],bty="n",cex=cex)
+ if (length(lgnd_kids)>0) legend(x=linfo$rect$left,y=linfo$rect$top-1*linfo$rect$h,horiz=T,legend=lgnd_kids,fill=cols[indkids],bty="n",cex=cex)
+ plot(1,1,xlab="",ylab="",xlim = rt_rng,ylim = int_rng,type="n")
- ## Plot eic across the directory set.
+ ## Plot eic across the directory set.
for (n in seq(length(dfs))) {
df <- dfs[[n]]
col <- cols[[n]]
@@ -472,12 +469,13 @@ presc.plot <- function(wd,mode,out="prescreen.pdf",pal="Dark2",cex=0.75,rt_digit
lines(intensity ~ rt,data=dfs_kids[[k]],type="h",col=cols_kids[[k]])
}
}
-
title(main=paste("ID:",i,"Ion m:",formatC(masses[[i]],digits=m_digits,format="f")),xlab="retention time [min]",ylab="intensity")
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)
+
+
## RChemMass::renderSMILES.rcdk(smiles[[i]],coords=c(x1,y1,x2,y2))
gc()
}
--
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