From 9f60e1b6393793c9417e0a118c928eabed6db6f6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Wed, 31 Aug 2022 15:29:49 +0200
Subject: [PATCH] app, plotting, shiny-ui-base: Add intensity zooming.
---
R/plotting.R | 11 ++++++++---
R/shiny-ui-base.R | 41 +++++++++++++++++++++++++++++++++++++++--
inst/rmd/app.Rmd | 20 ++++++++++++++++++++
3 files changed, 67 insertions(+), 5 deletions(-)
diff --git a/R/plotting.R b/R/plotting.R
index 56f6284..c6e6d45 100644
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -525,7 +525,7 @@ 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, asp=1) {
+make_eic_ms1_plot <- function(extr_ms1,summ,kvals,labs,axis="linear",rt_range=NULL,i_range=NULL, asp=1) {
## Get metadata.
summ_rows <- narrow_summ(summ,kvals,labs,"mz","ms1_rt","ms1_int","Name","SMILES","Formula")
## Get the table with ms1 data.
@@ -533,7 +533,12 @@ make_eic_ms1_plot <- function(extr_ms1,summ,kvals,labs,axis="linear",rt_range=NU
key <- names(kvals)
## Deal with retention time range.
- rt_lim <- if (is.null(rt_range)) NULL else ggplot2::coord_cartesian(xlim=rt_range)#ggplot2::xlim(rt_range[[1]],rt_range[[2]])
+ coord <- if (is.null(rt_range) && is.null(i_range)) {
+ NULL
+ } else {
+ ggplot2::coord_cartesian(xlim=rt_range,
+ ylim=i_range)
+ }
xrng <- range(pdata$rt) #if (!is.null(rt_range)) rt_range else range(pdata$rt)
dx <- abs(xrng[[2]]-xrng[[1]])
yrng <- range(pdata$intensity)
@@ -552,7 +557,7 @@ make_eic_ms1_plot <- function(extr_ms1,summ,kvals,labs,axis="linear",rt_range=NU
ggplot2::xlab("retention time")+
cust_geom_line()+
scale_y(axis=axis,labels=sci10)+
- rt_lim
+ coord
## annt_dx <- 5*dx/100.
## annt <- summ_rows[,.(x=..annt_dx+ms1_rt,y=ms1_int,txt=signif(ms1_rt,5))]
## ## Annotate.
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index d7a2b4a..a10305f 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -795,6 +795,16 @@ mk_shinyscreen_server <- function(projects,init) {
if (is.na(x2)) x2 <- NA_real_
c(x1,x2)
})
+
+ rf_get_irange <- reactive({
+ y1 <- input$plot_i_min
+ y2 <- input$plot_i_max
+
+ if (is.na(y1)) y1 <- NA_real_
+ if (is.na(y2)) y2 <- NA_real_
+ c(y1,y2)
+
+ })
rf_plot_eic_ms1 <- reactive({
isolate({
ms1 <- rvs$m$extr$ms1
@@ -806,7 +816,18 @@ mk_shinyscreen_server <- function(projects,init) {
make_eic_ms1_plot(ms1,summ,kvals=req(rf_get_cindex_kval()),
labs=req(rf_get_cindex_labs()),
asp=PLOT_EIC_ASPECT,
- rt_range=rf_get_rtrange())
+ rt_range=rf_get_rtrange(),
+ i_range=rf_get_irange())
+ })
+
+ rf_get_ms2_eic_rtrange <- reactive({
+ pms1 <- rf_plot_eic_ms1()
+ drng <- range(pms1$data$rt)
+ urng <- rf_get_rtrange()
+ if (is.na(urng[[1]])) urng[[1]] <- drng[[1]]
+ if (is.na(urng[[2]])) urng[[2]] <- drng[[2]]
+ print(urng)
+ urng
})
rf_plot_eic_ms2 <- reactive({
@@ -821,7 +842,7 @@ mk_shinyscreen_server <- function(projects,init) {
make_eic_ms2_plot(summ,
kvals=rf_get_cindex_kval(),
labs=rf_get_cindex_labs(),
- rt_range = rf_get_rtrange(),
+ rt_range = rf_get_ms2_eic_rtrange(),
asp=PLOT_EIC_ASPECT)
@@ -1365,12 +1386,22 @@ mk_shinyscreen_server <- function(projects,init) {
observeEvent(input$plot_brush,{
xmin <- input$plot_brush[["xmin"]]
xmax <- input$plot_brush[["xmax"]]
+ ymin <- input$plot_brush[["ymin"]]
+ ymax <- input$plot_brush[["ymax"]]
+
if (!is.null(xmin)) updateNumericInput(session=session,
inputId="plot_rt_min",
value=xmin)
if (!is.null(xmax)) updateNumericInput(session=session,
inputId="plot_rt_max",
value=xmax)
+
+ if (!is.null(ymin)) updateNumericInput(session=session,
+ inputId="plot_i_min",
+ value=ymin)
+ if (!is.null(ymax)) updateNumericInput(session=session,
+ inputId="plot_i_max",
+ value=ymax)
session$resetBrush("plot_brush")
},label = "get_rt_from_selection")
@@ -1384,6 +1415,12 @@ mk_shinyscreen_server <- function(projects,init) {
updateNumericInput(session=session,
inputId="plot_rt_max",
value=NA_real_)
+ updateNumericInput(session=session,
+ inputId="plot_i_min",
+ value=NA_real_)
+ updateNumericInput(session=session,
+ inputId="plot_i_max",
+ value=NA_real_)
}, label = "reset_rt_range")
diff --git a/inst/rmd/app.Rmd b/inst/rmd/app.Rmd
index eb15085..a69f489 100644
--- a/inst/rmd/app.Rmd
+++ b/inst/rmd/app.Rmd
@@ -692,6 +692,26 @@ numericInput(inputId = "plot_rt_max",
```
</div> <!-- RT div -->
+
+#### Intensity Range (MS1)
+
+<div style="display:flex; flex-direction: row;"> <!-- Intensity div -->
+```{r, echo=F}
+numericInput(inputId = "plot_i_min",
+ label="Start",
+ value=NA_real_,
+ width="15%")
+```
+```{r, echo=F}
+numericInput(inputId = "plot_i_max",
+ label="End",
+ value=NA_real_,
+ width="15%")
+
+
+```
+</div> <!-- Intensity div -->
+
</div>
<div>
```{r, echo=F}
--
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