From dd266151a865464f5e8f23e3a57b6e30a2ec18c4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Tue, 16 Aug 2022 16:44:54 +0200
Subject: [PATCH] app: Added report functionality.
---
R/plotting.R | 9 ++---
R/shiny-ui-base.R | 89 +++++++++++++++++++++++++++++++++++++++++++++++
inst/rmd/app.Rmd | 18 ++++++++++
3 files changed, 112 insertions(+), 4 deletions(-)
diff --git a/R/plotting.R b/R/plotting.R
index eff4b0a..e1b17df 100644
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -491,6 +491,7 @@ guide_fun <- function() {
narrow_summ <- function(summ,kvals,labs,...) {
keys <- names(kvals)
+ ## keys <- keys[!is.na(keys)]
needed <- setdiff(labs,keys)
x <- as.list(c(needed,...))
x <- c(list(summ,kvals),x)
@@ -498,8 +499,6 @@ narrow_summ <- function(summ,kvals,labs,...) {
}
make_eic_ms1_plot <- function(extr_ms1,summ,kvals,labs,axis="linear",rt_range=NULL, asp=1) {
-
- message("RTs: ", paste0(rt_range,coll=','))
## Get metadata.
summ_rows <- narrow_summ(summ,kvals,labs,"mz","ms1_rt","ms1_int","Name","SMILES","Formula")
## Get the table with ms1 data.
@@ -613,9 +612,11 @@ make_spec_ms2_plot <- function(extr_ms2,summ,kvals,labs,axis="linear",asp=1) {
}
-combine_plots <- function(p_eic_ms1,p_eic_ms2,p_spec_ms2) {
- cowplot::plot_grid(p_eic_ms1,p_eic_ms2,p_spec_ms2,ncol=1,align='vh',axis='b')
+combine_plots <- function(p_eic_ms1,p_eic_ms2,p_spec_ms2,p_struct) {
+ cowplot::plot_grid(p_eic_ms1,p_struct,p_eic_ms2,p_spec_ms2,ncol=2,align='v',axis='l')
}
+
+
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index 6270044..9aa1aba 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -1140,6 +1140,71 @@ mk_shinyscreen_server <- function(projects,init) {
rvs$gui$datatab$adduct <- z$adduct
}, label = "datatab-edit")
+ observeEvent(input$make_report_b,{
+ isolate({
+ ms1 <- rvs$m$extr$ms1
+ ms2 <- rvs$m$extr$ms2
+ summ <- rvs$m$out$tab$summ
+
+ })
+ req(NROW(summ)>0L)
+ req(NROW(ms1)>0L)
+ req(NROW(ms2)>0L)
+
+ cind <- rf_get_cindex()
+ key <- rf_get_cindex_key()
+ rt_range <- rf_get_rtrange()
+ labs <- req(rf_get_cindex_labs())
+ projdir <- rvs$gui$paths$project
+ fn <- paste0(file.path(projdir,input$report_name),'.pdf')
+ print(fn)
+ pdf(file=fn,paper="a4")
+ for (ri in 1:NROW(cind)) {
+ rowtab <- cind[ri][,..key]
+ kvals <- lapply(rowtab,function (x) x[[1]])
+ names(kvals) <- key
+ message('Compound index row: ',ri)
+ p1 <- make_eic_ms1_plot(ms1,summ,kvals=kvals,
+ labs=labs,
+ asp=PLOT_EIC_ASPECT,
+ rt_range=rt_range)
+ p2 <- make_eic_ms2_plot(summ,
+ kvals=kvals,
+ labs=labs,
+ rt_range = rt_range,
+ asp=PLOT_EIC_ASPECT)
+
+ id <- rowtab <- cind[ri][,..key][["ID"]][[1]]
+ smi <- rvs$m$out$tab$comp[ID==(id),SMILES][[1]]
+ grb <- smiles2img(smi)
+ p_struc <- qplot(1:5, 2*(1:5), geom="blank") +
+ annotation_custom(grb, xmin=-Inf, xmax=Inf, ymin=-Inf, ymax=Inf) +
+ theme_empty
+
+ p_spec <- make_spec_ms2_plot(ms2,
+ summ,
+ kvals=kvals,
+ labs=labs)
+
+ cmb <- combine_plots(p1,p2,p_spec,p_struc)
+ print(cmb)
+ }
+ dev.off()
+ })
+
+ ## observeEvent(input$plot_save_single,{
+
+ ## p1 <- rf_plot_eic_ms1()
+ ## p2 <- rf_plot_eic_ms2()
+ ## p3 <- rf_plot_spec_ms2()
+ ## str <- rf_plot_struct()
+
+ ## message("Plots saved to ",file.path(rvs$gui$paths$project,
+ ## FIG_TOPDIR))
+
+
+ ## })
+
## RENDER
output$curr_proj <- renderText({
@@ -1287,6 +1352,30 @@ mk_shinyscreen_server <- function(projects,init) {
## },height=1000)
+ observeEvent(input$plot_brush,{
+ xmin <- input$plot_brush[["xmin"]]
+ xmax <- input$plot_brush[["xmax"]]
+ if (!is.null(xmin)) updateNumericInput(session=session,
+ inputId="plot_rt_min",
+ value=xmin)
+ if (!is.null(xmax)) updateNumericInput(session=session,
+ inputId="plot_rt_max",
+ value=xmax)
+ session$resetBrush("plot_brush")
+
+ },label = "get_rt_from_selection")
+
+ observeEvent(input$plot_rt_click,
+ {
+ ## TODO: update to sensible range.
+ updateNumericInput(session=session,
+ inputId="plot_rt_min",
+ value=NA_real_)
+ updateNumericInput(session=session,
+ inputId="plot_rt_max",
+ value=NA_real_)
+ }, label = "reset_rt_range")
+
output$plot_eic_ms1 <- renderPlot({
rf_plot_eic_ms1()
diff --git a/inst/rmd/app.Rmd b/inst/rmd/app.Rmd
index 448b37e..7445af5 100644
--- a/inst/rmd/app.Rmd
+++ b/inst/rmd/app.Rmd
@@ -705,6 +705,24 @@ plotOutput("plot_spec_ms2",
</div>
<div></div>
</div>
+<div style="display: flex-flow: row nowrap"> <!-- Control Bar -->
+```{r, echo=F}
+## actionButton("plot_save_single",
+## label="Save this plot")
+## actionButton("plot_save_all",
+## label="Save all plots")
+actionButton("make_report_b",
+ label="Create report")
+textInput("report_name",
+ label="Report Name",
+ value="report")
+## textInput("plot_ext",
+## label = "Plot extension",
+## value = "pdf")
+```
+
+</div> <\!-- Control Bar -\-> -->
+
<!-- <div style="display: flex-flow: column nowrap"> <\!-- Main -\-> -->
<!-- <div style="display: flex; flex-direction: row; flex-wrap: nowrap;"> <\!-- EICs and Structure -\-> -->
--
GitLab