From 56a0459222abfd8d47dfd22c15354f531190aaa9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Fri, 14 Apr 2023 21:07:03 +0200
Subject: [PATCH] Clean up some comments in `make_spec_ms2_plot'.
---
R/plotting.R | 17 +++++------------
1 file changed, 5 insertions(+), 12 deletions(-)
diff --git a/R/plotting.R b/R/plotting.R
index e7ad265..568f425 100644
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -457,25 +457,18 @@ make_spec_ms2_plot <- function(db,summ,kvals,labs,axis="linear",asp=1, colrdata=
outcols=union(names(kvals),
colnames(summ)))[ms2_sel==T]
- spectra = db$extr$spectra[db$extr$cgm$ms2[,unique(.SD),
- .SDcols=c("ce","scan","rt")],
- on=.(scan),c("ce","rt"):=.(i.ce,i.rt)]
- subxdata = get_data_from_key(db=db,
- tab=spectra,
- kvals=kvals,
- outcols=c("catid","ce","mz","scan","rt","intensity"))
+ spectra = db$extr$spectra[mdata,on=.(precid,scan),.(catid,ce,mz,scan,rt=i.ms2_rt,intensity)]
if (NROW(mdata)==0L) return(NULL)
- if (NROW(subxdata) == 0L) return(NULL)
- ans = data.table(scan=mdata[,unique(scan)],key="scan")
+ if (NROW(spectra) == 0L) return(NULL)
- meta = db$cat[subxdata[,.(catid=unique(catid))],
+ meta = db$cat[spectra[,.(catid=unique(catid))],
on=.(catid),
.SD,
by=.EACHI,
.SDcols=labs]
- subxdata = meta[subxdata,on=.(catid),nomatch=NULL]
+ subxdata = meta[spectra,on=.(catid),nomatch=NULL]
@@ -485,7 +478,7 @@ make_spec_ms2_plot <- function(db,summ,kvals,labs,axis="linear",asp=1, colrdata=
if (NROW(pdata)==0L) return(NULL)
# Aspect ratio.
- xrng = range(pdata$mz)
+ xrng = range(pdata$mz,na.rm=T)
dx = abs(xrng[[2]]-xrng[[1]])
yrng = range(pdata$intensity)
dy = abs(yrng[[2]]-yrng[[1]])
--
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