From cd65df81c1524a6fe5d3c74f822cf28fee991127 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Sat, 15 Apr 2023 10:08:28 +0200
Subject: [PATCH] The output `print_spec_tab' now adapted to new data model.
* shiny-ui-base(gen_cindex, gen_summ_subset): Adapted. Function
`gen_cindex' now returns less confusing output.
* plotting(get_data_from_key): Argument `outcols' now has a default
NULL value.
---
R/plotting.R | 5 +++--
R/shiny-state.R | 20 ++++++++++++--------
R/shiny-ui-base.R | 8 +++++---
3 files changed, 20 insertions(+), 13 deletions(-)
diff --git a/R/plotting.R b/R/plotting.R
index 568f425..93ababd 100644
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -194,7 +194,7 @@ mk_logic_exp <- function(rest,sofar=NULL) {
}
-get_data_from_key <- function(db,tab,kvals,outcols) {
+get_data_from_key <- function(db,tab,kvals,outcols=NULL) {
## Ensure only names that exist in cat are used in selection. Or,
## should we not do this?
@@ -209,7 +209,8 @@ get_data_from_key <- function(db,tab,kvals,outcols) {
## Get precids.
mztab = db$precursors[cattab,on="catid"]
outnames = union(valid_names,outcols)
- tab[mztab,on="precid"][,..outnames]
+ res = tab[mztab,on="precid"]
+ if (!is.null(outcols)) res[,..outnames] else res
}
diff --git a/R/shiny-state.R b/R/shiny-state.R
index c0b32f9..e943b10 100644
--- a/R/shiny-state.R
+++ b/R/shiny-state.R
@@ -495,11 +495,11 @@ gen_cindex <- function(summ,sorder,cols = CINDEX_COLS,by. = CINDEX_BY) {
xsumm <- summ[,..allc]
setnames(xsumm,old="ms1_rt",new="rt",skip_absent=T)
res <- xsumm[,.SD[max(qlt_ms1)==qlt_ms1][max(qlt_ms2)==qlt_ms2],by=by.]
- res <- res[,c("mz","rt","Name","qlt_ms1","qlt_ms2"):=.(first(mz),
- first(mean(rt)),
- first(Name),
- first(qlt_ms1),
- first(qlt_ms2)),
+ res <- res[,c("mz","rt","Name","qlt_ms1","qlt_ms2"):=.(mean(mz,na.rm=T),
+ mean(rt,na.rm=T),
+ first(Name),
+ max(qlt_ms1,na.rm=T),
+ max(qlt_ms2,na.rm=T)),
by=by.]
res <- res[,unique(.SD),by=by.]
@@ -518,7 +518,11 @@ gen_cindex <- function(summ,sorder,cols = CINDEX_COLS,by. = CINDEX_BY) {
ord[ind] <- -1L
}
if (length(sorder)>0) setorderv(res,cols=sorder,order=ord)
- setnames(res,old="rt",new="rt(ms1)")
+
+ ## Remove confusing columns.
+ res[,c("rt","mz"):=NULL]
+ res[,c("qlt_ms1","qlt_ms2"):=.(signif(100*qlt_ms1/10.,3),signif(100*qlt_ms2/10.,3))]
+ setnames(res,c("qlt_ms1","qlt_ms2"),c("best score (ms1)","best score (ms2)"))
res
}
@@ -554,9 +558,9 @@ get_cindex_kval <- function(cindex,row,key) {
res
}
-get_summ_subset <- function(summ,ptab,paritem,kvals) {
+get_summ_subset <- function(db,summ,ptab,paritem,kvals) {
select <- ptab[item==(paritem)]
- tab <- get_data_from_key(summ,kvals)[select,nomatch=NULL,on=key(ptab)]
+ tab <- get_data_from_key(db=db,tab=summ,kvals=kvals)[select,nomatch=NULL,on=key(ptab)]
if ("scan.1" %in% names(tab)) tab[,scan.1:=NULL] #TODO: This is
#probably a lousy
#hack.
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index 2b50752..a186eb4 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -760,7 +760,8 @@ mk_shinyscreen_server <- function(projects,init) {
kvals = req(rf_get_cindex_kval())
ptab = rf_get_cindex_parents()
if (isTruthy(parent)) {
- get_summ_subset(summ=summ,
+ get_summ_subset(db=rvs$m$db,
+ summ=summ,
ptab=ptab,
paritem=parent,
kvals=kvals)
@@ -1774,8 +1775,9 @@ mk_shinyscreen_server <- function(projects,init) {
#it.
key = unique(c(names(allval)[names(allval) %in% BASE_KEY_MS2],"scan"))
kval2 = allval[key]
- spec = get_data_from_key(ms2,kval2)[,.(mz,intensity)]
- ## as.character(lapply(1L:NROW(spec),function(nr) paste0(spec[nr,mz]," ",spec[nr,intensity])))
+ ## Only precid and scan can be used for selection in spectra.
+ kval2 = as.data.table(kval2[c("precid","scan")])
+ spec = rvs$m$db$extr$spectra[kval2,.(mz,intensity),on=.(precid,scan)]
print(as.data.frame(spec),row.names=F)
} else {
--
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