From 61ebfc23eec4de05a3ab0a4610239be4a075c6f0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Thu, 4 Aug 2022 17:28:41 +0200
Subject: [PATCH] app: Reintroduced structures.
---
R/plotting.R | 51 +++++++++++++++++---------------
R/resources.R | 2 ++
R/shiny-ui-base.R | 74 +++++++++++++++++++++++++++--------------------
inst/rmd/app.Rmd | 14 +++++++--
4 files changed, 84 insertions(+), 57 deletions(-)
diff --git a/R/plotting.R b/R/plotting.R
index 1fb7a4f..8644e0d 100644
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -348,7 +348,13 @@ theme_eic <- function(...) theme_light()+ggplot2::theme(axis.title=ggplot2::elem
legend.text=ggplot2::element_text(size=12L),
plot.caption=ggplot2::element_text(size=12L),...)
-
+theme_empty <- ggplot2::theme_bw()
+theme_empty$line <- ggplot2::element_blank()
+theme_empty$rect <- ggplot2::element_blank()
+theme_empty$strip.text <- ggplot2::element_blank()
+theme_empty$axis.text <- ggplot2::element_blank()
+theme_empty$plot.title <- ggplot2::element_blank()
+theme_empty$axis.title <- ggplot2::element_blank()
sci10 <- function(x) {
prefmt <- formatC(x,format="e",digits=2)
@@ -438,18 +444,21 @@ get_data_4_eic_ms1 <- function(extr_ms1,kvals,labs) {
}
## Prepare MS2 eic data: rt and intensity + key made of splitby.
-get_data_4_eic_ms2 <- function(summ,adduct,id,splitby) {
- key <- list(adduct=adduct,ID=id)
- tab <-get_data_from_key(tab=summ,key=key)
- pdata <- tab[,.(intensity=ms2_int,rt=ms2_rt),by=c('ID',splitby,"an")]
- 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_ms2 <- function(summ,kvals,labs) {
+ tab <-get_data_from_key(tab=summ,key=kvals)
+ nms <- names(kvals)
+ byby <- unique(c(nms,labs,"an"))
+ pdata <- tab[,.(intensity=ms2_int,rt=ms2_rt),by=byby]
+ if (NROW(pdata)==0L) return(NULL)
+ xlxx <- as.character(labs)
+ pdata <- eval(bquote(pdata[,label:=make_line_label(..(lapply(xlxx,as.symbol))),by=.(xlxx)],splice=T))
+ setkeyv(pdata,cols=c(labs,"rt"))
pdata
}
-make_eic_ms1_plot <- function(extr_ms1,summ,kvals,labs,axis="linear",rt_range=NULL) {
+make_eic_ms1_plot <- function(extr_ms1,summ,kvals,labs,axis="linear",rt_range=NULL, asp=0.5) {
## Get the table with ms1 data.
@@ -465,7 +474,7 @@ make_eic_ms1_plot <- function(extr_ms1,summ,kvals,labs,axis="linear",rt_range=NU
dy <- abs(yrng[[2]]-yrng[[1]])
## Calculate aspect ratio.
- aspr <- if (dx < .Machine$double.eps) 1 else 0.5*as.numeric(dx)/as.numeric(dy)
+ aspr <- if (dx < .Machine$double.eps) 1 else asp*as.numeric(dx)/as.numeric(dy)
tag_txt = paste0(sapply(names(kvals),function (nx) paste0(nx,": ", kvals[[nx]])),
@@ -486,22 +495,17 @@ make_eic_ms1_plot <- function(extr_ms1,summ,kvals,labs,axis="linear",rt_range=NU
}
-make_eic_ms2_plot <- function(summ,key,splitby,axis="linear",rt_range=NULL) {
- set <- key[['set']]
- id <- key[['id']]
- adduct <- key[['adduct']]
- key <- list(set=set,
- adduct=adduct,
- ID=id)
-
+make_eic_ms2_plot <- function(summ,kvals,labs,axis="linear",rt_range=NULL,asp=0.5) {
+ ## TODO
## Get plotting data for the compound.
pdata <- get_data_4_eic_ms2(summ,
- adduct=adduct,
- id=id,
- splitby=splitby)
+ kvals=kvals,
+ labs=labs)
+
+ if (NROW(pdata)==0L) return(NULL)
## Get metadata.
- summ_row <- get_data_from_key(summ,key=key)
+ summ_row <- get_data_from_key(summ,key=kvals)
## Deal with retention time range.
rt_lim <- if (is.null(rt_range)) NULL else ggplot2::xlim(rt_range)
@@ -511,10 +515,11 @@ make_eic_ms2_plot <- function(summ,key,splitby,axis="linear",rt_range=NULL) {
dy <- abs(yrng[[2]]-yrng[[1]])
## Fix aspect ratio.
- aspr <- if (dx < .Machine$double.eps) 1 else 0.5*as.numeric(dx)/as.numeric(dy)
+ aspr <- if (dx < .Machine$double.eps) 1 else asp*as.numeric(dx)/as.numeric(dy)
## Derive various labels.
- tag_txt = paste0("Set: ", set, " ID: ",id)
+ tag_txt = paste0(sapply(names(kvals),function (nx) paste0(nx,": ", kvals[[nx]])),
+ collapse='; ')
title_txt = paste0("MS2 EIC for ion m/z = ",paste0(signif(unique(summ_row$mz),digits=7L),collapse=", "))
subt_txt = if (!length(summ_row$Name)==0L && !is.na(summ_row$Name) && nchar(summ_row$Name)>0L) summ_row$Name else NULL
## Base plot.
diff --git a/R/resources.R b/R/resources.R
index 8ff85ef..4c3b5d3 100644
--- a/R/resources.R
+++ b/R/resources.R
@@ -292,3 +292,5 @@ ARRANGE_CHOICES <- c(nothing="nothing",
mz="mz",
rt="rt",
id="ID")
+
+PLOT_EIC_ASPECT <- 0.75
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index 9ae0b4f..6477a3d 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -767,53 +767,59 @@ mk_shinyscreen_server <- function(projects,init) {
})
req(NROW(summ)>0L)
req(NROW(ms1)>0L)
- make_eic_ms1_plot(ms1,summ,kvals=req(rf_get_cindex_kval()),labs=req(rf_get_cindex_labs()))
+ make_eic_ms1_plot(ms1,summ,kvals=req(rf_get_cindex_kval()),
+ labs=req(rf_get_cindex_labs()),
+ asp=PLOT_EIC_ASPECT)
})
rf_plot_eic_ms2 <- reactive({
isolate({
summ <- rvs$m$out$tab$summ
- cind <- rf_get_cindex()
})
req(NROW(summ)>0L)
- req(NROW(cind)>0L)
- row <- input$cindex_row_last_clicked
- req(row)
- sel <- cind[row]
+
gg <- rf_plot_eic_ms1()
rt_rng <- range(gg$data$rt)
make_eic_ms2_plot(summ,
- key=rf_get_cindex_kval(),
- splitby=c("tag"),
- rt_range = rt_rng)
+ kvals=rf_get_cindex_kval(),
+ labs=rf_get_cindex_labs(),
+ rt_range = rt_rng,
+ asp=PLOT_EIC_ASPECT)
})
- rf_plot_spec_ms2 <- reactive({
- isolate({
- summ <- rvs$m$out$tab$summ
- ms2 <- rvs$m$extr$ms2
- cind <- rf_get_cindex()
- })
- req(NROW(summ)>0L)
- req(NROW(ms2)>0L)
+ rf_plot_struct <- reactive({
+ cind <- rf_get_cindex()
+ key <- rf_get_cindex_key()
req(NROW(cind)>0L)
- row <- input$cindex_row_last_clicked
- req(row)
- sel <- cind[row]
-
- make_spec_ms2_plot(ms2,
- summ,
- set=sel$set,
- adduct=sel$adduct,
- id=sel$ID,
- splitby=c("adduct","tag"))
-
-
- })
+ row <- req(input$cindex_row_last_clicked)
+ id <- rowtab <- cind[row][,..key][["ID"]][[1]]
+ smi <- rvs$m$out$tab$comp[ID==(id),SMILES][[1]]
+ print("smiles:")
+ print(smi)
+ grb <- smiles2img(smi)
+ xx <- qplot(1:5, 2*(1:5), geom="blank") +
+ annotation_custom(grb, xmin=-Inf, xmax=Inf, ymin=-Inf, ymax=Inf) +
+ theme_empty
+ xx
+ })
+
+ ## rf_plot_spec_ms2 <- reactive({
+ ## isolate({
+ ## summ <- rvs$m$out$tab$summ
+ ## ms2 <- rvs$m$extr$ms2
+ ## })
+ ## req(NROW(summ)>0L)
+ ## req(NROW(ms2)>0L)
+ ## req(NROW(cind)>0L)
+ ## make_spec_ms2_plot(ms2,
+ ## summ,
+ ## kvals=req(rf_get_cindex_kval()),
+ ## labs=req(rf_get_cindex_labs()))
+ ## })
## OBSERVERS
@@ -1227,9 +1233,13 @@ mk_shinyscreen_server <- function(projects,init) {
output$plot_eic_combined <- renderPlot({
p1 <- rf_plot_eic_ms1()
- p2 <- NULL#rf_plot_eic_ms2()
+ p2 <- rf_plot_eic_ms2()
combine_plots(p1,p2)
})
+
+ output$plot_struct <- renderPlot({
+ rf_plot_struct()
+ })
## output$plot_eic_ms1 <- renderPlot({
## rf_plot_eic_ms1()
## })
@@ -1239,7 +1249,7 @@ mk_shinyscreen_server <- function(projects,init) {
## })
output$plot_spec_ms2 <- renderPlot({
- rf_plot_spec_ms2()
+ NULL #rf_plot_spec_ms2()
})
diff --git a/inst/rmd/app.Rmd b/inst/rmd/app.Rmd
index 5f3de6a..c9755f0 100644
--- a/inst/rmd/app.Rmd
+++ b/inst/rmd/app.Rmd
@@ -666,6 +666,8 @@ DT::DTOutput("cindex")
<div style="display: flex-flow: column nowrap">
### Viewer
+<div style="display: flex; flex-direction: row; flex-wrap: nowrap;">
+<div style="width: 70%;"> <!-- EIC ID Plot -->
```{r,echo=F}
## plotOutput("plot_eic_ms1",
## hover = hoverOpts(id="plot_hover",
@@ -693,14 +695,22 @@ plotOutput("plot_eic_combined",
dblclick = "plot_rt_click",
brush = "plot_brush")
+```
+</div> <!-- EIC ID Plot -->
+<div style="width: 30%;"> <!-- Structure -->
+```{r, echo=F}
+plotOutput("plot_struct")
+```
+</div>
+</div>
+```{r, echo=F}
+
plotOutput("plot_spec_ms2",
hover = hoverOpts(id="plot_hover",
delayType = "throttle",
delay=100),
dblclick = "plot_mz_click",
brush = brushOpts(id="plot_mz_brush"))
-
-
```
<div style="display: flex-flow: row nowrap"> <!-- Control Bar -->
--
GitLab