From 75f09bd5c04afdf72eb5a247c66a11c9288fc14f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Thu, 30 Mar 2023 00:15:20 +0200
Subject: [PATCH] Function make_eic_ms1_plot got a new argument `db'.
---
R/plotting.R | 9 ++++-----
R/shiny-ui-base.R | 34 +++++++++++++++++++++-------------
2 files changed, 25 insertions(+), 18 deletions(-)
diff --git a/R/plotting.R b/R/plotting.R
index eb90abd..56f0541 100644
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -325,8 +325,7 @@ narrow_summ <- function(summ,kvals,labs,...) {
### PLOTTING: TOP-LEVEL PLOT CREATION
-make_eic_ms1_plot <- function(extr_ms1,summ,kvals,labs,axis="linear",rt_range=NULL,i_range=NULL, asp=1,colrdata=NULL) {
-
+make_eic_ms1_plot <- function(db,extr_ms1,summ,kvals,labs,axis="linear",rt_range=NULL,i_range=NULL, asp=1,colrdata=NULL) {
## If nothing selected, just return NULL.
if (is.null(kvals)) return(NULL)
@@ -336,7 +335,7 @@ make_eic_ms1_plot <- function(extr_ms1,summ,kvals,labs,axis="linear",rt_range=NU
## TODO: FIXME: Somehow calculating representationve ms1_rt for
## plots is wrong. Horrible and wrong. Will remove those labels
## until we fix.
- summ_rows <- narrow_summ(summ,kvals,labs,"mz","ms1_rt","ms1_int","Name","SMILES","Formula","qa_ms1_exists","scan","ms2_sel")
+ summ_rows <- narrow_summ(summ,kvals,labs,"mz","ms1_rt","ms1_int","Name","SMILES","qa_ms1_exists","scan","ms2_sel")
rows_key <- union(data.table::key(summ_rows),labs)
summ_rows$sel_ms1_rt=NA_real_
summ_rows[ms2_sel==T,sel_ms1_rt:=ms1_rt[which.max(ms1_int)],by=rows_key]
@@ -388,7 +387,7 @@ make_eic_ms2_plot <- function(summ,kvals,labs,axis="linear",rt_range=NULL,asp=1,
if (is.null(kvals)) return(NULL)
## Get metadata.
- summ_rows <- narrow_summ(summ,kvals,labs,"mz","ms2_rt","ms2_int","Name","SMILES","Formula")
+ summ_rows <- narrow_summ(summ,kvals,labs,"mz","ms2_rt","ms2_int","Name","SMILES")
## Get plotting data for the compound.
pdata <- get_data_4_eic_ms2(summ,
@@ -436,7 +435,7 @@ make_spec_ms2_plot <- function(extr_ms2,summ,kvals,labs,axis="linear",asp=1, col
if (NROW(mdata)==0L) return(NULL)
if (NROW(subxdata) == 0L) return(NULL)
ans <- data.table(scan=mdata[,unique(scan)],key="scan")
- ms2ctg <- c(intersect(c(names(kvals),labs),names(extr_ms2)),"CE")
+ ms2ctg <- c(intersect(c(names(kvals),labs),names(extr_ms2)),"ce")
xlxx <- intersect(as.character(labs),names(extr_ms2))
common_labels <- unique(c("scan",common_key,intersect(names(extr_ms2),labs)))
pdata <- subxdata[ans,on="scan"][,.(mz=mz,intensity=intensity,rt=signif(unique(rt),5)),by=common_labels]
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index 3ea38e7..8609042 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -815,18 +815,22 @@ mk_shinyscreen_server <- function(projects,init) {
isolate({
ms1 = rvs$m$db$extr$cgm$ms1
summ = rvs$m$out$tab$summ
+ db = rvs$m$db
})
req(NROW(summ)>0L)
req(NROW(ms1)>0L)
- p = make_eic_ms1_plot(ms1,summ,kvals=rf_get_cindex_kval(),
- labs=rf_get_cindex_labs(),
- asp=PLOT_EIC_ASPECT,
- rt_range=rf_get_rtrange(),
- i_range=rf_get_irange(),
- colrdata = rf_colrdata())
+ p = make_eic_ms1_plot(db=db,
+ extr_ms1=ms1,
+ summ,
+ kvals=rf_get_cindex_kval(),
+ labs=rf_get_cindex_labs(),
+ asp=PLOT_EIC_ASPECT,
+ rt_range=rf_get_rtrange(),
+ i_range=rf_get_irange(),
+ colrdata = rf_colrdata())
p = if (!is.null(p)) p else empty_plot("Nothing to plot")
@@ -1148,7 +1152,7 @@ mk_shinyscreen_server <- function(projects,init) {
rv_extr_flag(F)
rvs$m = run(m=rvs$m,
envopts=init$envopts,
- phases=c("setup","comptab","extract"))
+ phases=c("setup","comptab","db","extract"))
rvs$status$is_extracted_stat = "Yes."
rvs$status$is_qa_stat = "No."
fn_c_state = file.path(rvs$m$run$paths$project,
@@ -1299,6 +1303,7 @@ mk_shinyscreen_server <- function(projects,init) {
ms1 = rvs$m$db$extr$cgm$ms1
ms2 = rvs$m$db$extr$cgm$ms2
summ = rvs$m$out$tab$summ
+ db = rvs$m$db
})
req(NROW(summ)>0L)
@@ -1320,12 +1325,15 @@ mk_shinyscreen_server <- function(projects,init) {
names(kvals) = key
message('Compound index row: ',ri)
- p1 = make_eic_ms1_plot(ms1,summ,kvals=kvals,
- labs=labs,
- asp=PLOT_EIC_ASPECT,
- rt_range=rt_range,
- i_range=i_range,
- colrdata = colrdata) + theme_print()
+ p1 = make_eic_ms1_plot(db=db,
+ ms1,
+ summ,
+ kvals=kvals,
+ labs=labs,
+ asp=PLOT_EIC_ASPECT,
+ rt_range=rt_range,
+ i_range=i_range,
+ colrdata = colrdata) + theme_print()
p2 = make_eic_ms2_plot(summ,kvals=kvals,
labs=labs,
--
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