From be2fe1a6bfd0f54b17d3e7fc37ddcdf3b881b0c8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Fri, 15 Jul 2022 16:23:29 +0200
Subject: [PATCH] ...
---
R/plotting.R | 47 ++++++++++++++++++++++++++---------------------
R/resources.R | 5 +++--
R/shiny-ui-base.R | 8 ++++++--
3 files changed, 35 insertions(+), 25 deletions(-)
diff --git a/R/plotting.R b/R/plotting.R
index 55a3c15..5d0eb90 100644
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -397,17 +397,28 @@ get_data_from_key <- function(tab,key) {
eval(bquote(tab[.(skey)]))
}
+
+get_label_group <- function(key) {
+ message('CINDEX:',paste0(CINDEX_BY,coll=','))
+ message('key:', paste0(key,coll=','))
+ setdiff(CINDEX_BY,key)
+}
+
make_line_label <- function(...) {
paste(...,sep="; ")
}
## Prepare MS1 eic data: rt and intensity + key made of splitby.
-get_data_4_eic_ms1 <- function(extr_ms1,adduct,id,splitby) {
- key <- list(adduct=adduct,ID=id)
- tab <-get_data_from_key(tab=extr_ms1,key=key)
- pdata <- tab[,.(rt,intensity),by=c('ID',splitby)]
- pdata <- eval(bquote(pdata[,label:=make_line_label(..(lapply(splitby,as.symbol))),by=.(splitby)],splice=T))
- setkeyv(pdata,cols=c("ID",splitby,"rt"))
+get_data_4_eic_ms1 <- function(extr_ms1,key) {
+ actual_key <- key[intersect(names(key),names(extr_ms1))]
+ label_group <- intersect(get_label_group(names(key)),names(extr_ms1))
+ tab <-get_data_from_key(tab=extr_ms1,key=actual_key)
+ label_group <- as.list(label_group)
+ names(label_group) <- NULL
+ pdata <- tab[,.(rt,intensity),by=label_group]
+
+ pdata <- eval(bquote(pdata[,label:=make_line_label(..(lapply(label_group,as.symbol))),by=(label_group)],splice=T))
+ setkeyv(pdata,cols=unique(c("ID",as.character(label_group),"rt")))
pdata
}
@@ -423,16 +434,11 @@ get_data_4_eic_ms2 <- function(summ,adduct,id,splitby) {
-make_eic_ms1_plot <- function(extr_ms1,summ,set,adduct,id,splitby,axis="linear",rt_range=NULL) {
- key <- list(set=set,
- adduct=adduct,
- ID=id)
+make_eic_ms1_plot <- function(extr_ms1,summ,key,axis="linear",rt_range=NULL) {
+
## Get the table with ms1 data.
- pdata <- get_data_4_eic_ms1(extr_ms1,
- adduct=adduct,
- id=id,
- splitby=splitby)
+ pdata <- get_data_4_eic_ms1(extr_ms1, key)
## Get metadata.
summ_row <- get_data_from_key(summ,key=key)
@@ -452,8 +458,8 @@ make_eic_ms1_plot <- function(extr_ms1,summ,set,adduct,id,splitby,axis="linear",
title_txt = paste0("MS1 EIC for ion m/z = ",paste0(signif(unique(summ_row$mz),digits=7L),collapse=", "))
nm <- paste(unique(summ_row$Name),collapse="; ")
subt_txt = if (!length(nm)==0L && !is.na(nm) && nchar(nm)>0L) nm else NULL
- p <- ggplot2::ggplot(pdata,aes(x=rt,y=intensity,colour=label))+ggplot2::labs(caption=tag_txt,title=title_txt,subtitle=subt_txt)+ggplot2::xlab("retention time")+ggplot2::geom_line()+ggplot2::coord_fixed(ratio=aspr)+scale_y(axis=axis,labels=sci10)+rt_lim
-
+ p <- ggplot2::ggplot(pdata,aes(x=rt,y=intensity,colour=label))+ggplot2::labs(caption=tag_txt,title=title_txt,subtitle=subt_txt)+ggplot2::xlab("retention time")+ggplot2::geom_line()+scale_y(axis=axis,labels=sci10)+rt_lim
+ ## +ggplot2::coord_fixed(ratio=aspr)
annt_dx <- 5*dx/100.
annt <- summ[summ_row,on=names(key),nomatch=NULL][,.(x=..annt_dx+ms1_rt,y=ms1_int,txt=signif(ms1_rt,5))]
@@ -465,7 +471,7 @@ make_eic_ms1_plot <- function(extr_ms1,summ,set,adduct,id,splitby,axis="linear",
}
-make_eic_ms2_plot <- function(summ,set,adduct,id,splitby,axis="linear",rt_range=NULL) {
+make_eic_ms2_plot <- function(summ,key,splitby,axis="linear",rt_range=NULL) {
key <- list(set=set,
adduct=adduct,
ID=id)
@@ -497,8 +503,8 @@ make_eic_ms2_plot <- function(summ,set,adduct,id,splitby,axis="linear",rt_range=
p <- ggplot2::ggplot(pdata,aes(x=rt,ymin=0,ymax=intensity,colour=label)) +
ggplot2::labs(caption=tag_txt,title=title_txt,subtitle=subt_txt) +
ggplot2::xlab("retention time")+ggplot2::ylab("intensity")+ggplot2::geom_linerange()+
- ggplot2::coord_fixed(ratio=aspr)+scale_y(axis=axis,labels=sci10)+rt_lim
-
+ scale_y(axis=axis,labels=sci10)+rt_lim
+ ## ggplot2::coord_fixed(ratio=aspr)+
ans <- pdata[,unique(an)]
annt_dx <- 5*dx/100.
annt <- summ[an %in% (ans),.(an=an,x=ms2_rt+..annt_dx,y=1.1*ms2_int,txt=signif(ms2_rt,5))]
@@ -545,8 +551,7 @@ make_spec_ms2_plot <- function(extr_ms2,summ,set,adduct,id,splitby,axis="linear"
}
combine_plots <- function(p_eic_ms1,p_eic_ms2) {
- pl <- list(p_eic_ms1,p_eic_ms2)
- cowplot::plot_grid(pl,ncol=1,align='v')
+ cowplot::plot_grid(p_eic_ms1,p_eic_ms2,ncol=1,align='v',axis='b')
}
diff --git a/R/resources.R b/R/resources.R
index a691fad..35f3481 100644
--- a/R/resources.R
+++ b/R/resources.R
@@ -283,11 +283,12 @@ CMPD_LIST_PATT <- "((*.csv)|(*.csv.gz))$"
SET_LIST_PATT <- CMPD_LIST_PATT
DFILES_LIST_PATT <- ".*\\.mz[Mm][Ll]$"
-CINDEX_BY <- c("set","ID","adduct","tag")
+CINDEX_BY <- c("set","ID","tag","adduct")
CINDEX_COLS <- c("mz", "ms1_rt","Name","qa_ms1","qa_ms2")
ARRANGE_CHOICES <- c(nothing="nothing",
quality="quality",
set="set",
adduct="adduct",
mz="mz",
- rt="rt")
+ rt="rt",
+ id="ID")
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index 985951a..f833950 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -704,9 +704,13 @@ mk_shinyscreen_server <- function(projects,init) {
m$input$tab$setid
})
+ rf_cindex_key <- reactive({
+ if (isTruthy(input$cindex_group)) setdiff(CINDEX_BY,input$cindex_group) else CINDEX_BY
+ })
+
rf_get_cindex <- reactive({
rvs$status$is_qa_stat
- grp <- if (isTruthy(input$cindex_group)) setdiff(CINDEX_BY,input$cindex_group) else CINDEX_BY
+ grp <- rf_cindex_key()
s1 <- input$sort1
s2 <- input$sort2
s3 <- input$sort3
@@ -1183,7 +1187,7 @@ mk_shinyscreen_server <- function(projects,init) {
validate(need(NROW(tab)>0L,message="Need to prescreen, first."))
DT::datatable(tab,
rownames=NULL,
- options=list(filter=T),
+ options=list(filter=T,ordering=F,dom='t'),
selection="single")
})
--
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