From b8e3f9aa96c819c81b4717f8ca67e2ff255990ff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Thu, 26 Jan 2023 11:33:16 +0100
Subject: [PATCH] app: Restructuring Viewer
* app_results_explorer_cindex: New file.
* app_results_explorer_cindex_controls: New file.
---
R/api.R | 11 +-
R/shiny-ui-base.R | 25 ++-
inst/rmd/app.Rmd | 211 +-----------------
inst/rmd/app_config_and_status.Rmd | 3 +
inst/rmd/app_results_explorer_cindex.Rmd | 22 ++
.../app_results_explorer_cindex_controls.Rmd | 18 ++
inst/www/custom.css | 16 ++
7 files changed, 99 insertions(+), 207 deletions(-)
create mode 100644 inst/rmd/app_results_explorer_cindex.Rmd
create mode 100644 inst/rmd/app_results_explorer_cindex_controls.Rmd
diff --git a/R/api.R b/R/api.R
index 46e2f71..9dfd886 100644
--- a/R/api.R
+++ b/R/api.R
@@ -697,12 +697,17 @@ prepare_app <- function(dir_before,
dir_start <- tempfile("shinyscreen")
dir.create(dir_start, recursive = T)
+ ## Get list of app document contents.
+ dir_rmd = system.file("rmd",package = "shinyscreen")
+ fnms_rmd = list.files(dir_rmd,pattern = r"(^app.*\.Rmd$)",full.names=T)
+
## Copy startup files to that location.
dir.create(file.path(dir_start,'www'), showWarnings=F)
saveRDS(object = init,file=file.path(dir_start,"init.rds"))
- file.copy(system.file(file.path("rmd","app.Rmd"),package = "shinyscreen"),file.path(dir_start,"app_run.Rmd"))
- file.copy(system.file(file.path("rmd","app_config_and_status.Rmd"),package = "shinyscreen"),file.path(dir_start,"app_config_and_status.Rmd"))
+
file.copy(system.file(file.path("www","custom.css"),package = "shinyscreen"),file.path(dir_start,"www","custom.css"))
+ for (fn in fnms_rmd) file.copy(fn,file.path(dir_start,basename(fn)))
+
dir_start
}
@@ -736,7 +741,7 @@ app <- function(projects=getwd(),
on.exit(expr=setwd(dir_before))
setwd(dir_start)
- rmarkdown::run(file = "app_run.Rmd", shiny_args = shiny_args, render_args = render_args)
+ rmarkdown::run(file = "app.Rmd", shiny_args = shiny_args, render_args = render_args)
}
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index 8193bc7..3bbce3a 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -1213,13 +1213,36 @@ mk_shinyscreen_server <- function(projects,init) {
updateSelectInput(session=session,
inputId="mf_local_database",
choices=list.files(path=init$envopts$metfrag$db_dir,
- pattern=patt))
+ pattern=patt),
+ selected=character(0))
} else {
updateSelectInput(session=session,
inputId="mf_local_database",
choices=character(0))
}
}, label = "mf-database-type")
+
+ observeEvent(input$mf_local_database,{
+
+ fn = input$mf_local_database
+
+ if (length(fn) && nchar(fn)>0L) {
+ e = init$envopts
+ dbdir = e$metfrag$db_dir
+ fn = file.path(dbdir,fn)
+ dtnms = data.table::fread(file=fn,nrows=1L)
+ nms = names(dtnms)
+ updateSelectInput(session=session,
+ inputId="mf_local_db_col_ident",
+ choices = c(character(0),nms),
+ selected = character(0))
+ updateSelectInput(session=session,
+ inputId="mf_local_db_col_scores",
+ choices = c(character(0),nms),
+ selected = character(0))
+ }
+
+ }, label = "mf-local-database")
## OBSERVERS: VIEWER
diff --git a/inst/rmd/app.Rmd b/inst/rmd/app.Rmd
index bad1dcb..2cb33f0 100644
--- a/inst/rmd/app.Rmd
+++ b/inst/rmd/app.Rmd
@@ -394,212 +394,17 @@ actionButton(inputId = "presc_b",
## Results Explorer
-
-<div style="display: flex; flex-flow: column nowrap;">
-<div style="display: flex; flex-flow: column; padding-right:1.0em">
-
-### Compound Index
-
-```{r, echo=F}
-selectInput("cindex_group",label="Group",
- choices=c(NA_character_,
- "adduct","tag"),
- multiple=T,
- selected=c("adduct","tag"))
-```
-
-<div style="display: flex; flex-flow: row nowrap">
-```{r, echo=F}
-selectInput("sort1",label="Sort by ", choices=shinyscreen:::ARRANGE_CHOICES,width="15%",selected="quality")
-selectInput("sort2",label="then by ", choices=shinyscreen:::ARRANGE_CHOICES,width="15%",selected="mz")
-selectInput("sort3",label="then", choices=shinyscreen:::ARRANGE_CHOICES,width="15%")
-selectInput("sort4",label="and finally by", choices=shinyscreen:::ARRANGE_CHOICES,width="15%")
-```
-</div> <!-- Arrange -->
-
-<div>
-```{r, echo=F}
-DT::DTOutput("cindex")
-```
-
-</div> <!-- cindex -->
-
-</div> <!-- Compound Explorer Panel -->
-
-### Viewer
-
-<div class="plot-layout"> <!-- Plot Section -->
-<div>
-```{r, echo=F}
-plotOutput("plot_eic_ms1",
- hover = hoverOpts(id="plot_hover",
- delayType = "throttle",
- delay=100),
- dblclick = "plot_rt_click",
- brush = "plot_brush")
-```
-</div>
-<div>
-```{r, echo=F}
-plotOutput("plot_struct")
-```
-</div>
-<div>
-```{r, echo=F}
-plotOutput("plot_eic_ms2",
- hover = hoverOpts(id="plot_hover",
- delayType = "throttle",
- delay=100),
- dblclick = "plot_rt_click",
- brush = "plot_brush")
-```
-</div>
-<div>
-
-#### Tweak Plot Parameters
-
-```{r, echo=F}
-textOutput("plot_hover_out")
-```
-
-#### Retention Time Range
-
-<div style="display:flex; flex-direction: row;"> <!-- RT div -->
-```{r, echo=F}
-numericInput(inputId = "plot_rt_min",
- label="Start",
- value=NA_real_,
- width="30%")
+<div class='flex-layers'> <!-- cindex -->
+<div> <!-- cindex-cindex -->
+```{r, child='app_results_explorer_cindex.Rmd'}
```
-```{r, echo=F}
-numericInput(inputId = "plot_rt_max",
- label="End",
- value=NA_real_,
- width="30%")
-
-
-```
-</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="30%")
+</div> <!-- cindex-cindex -->
+<div> <!-- cindex-controls -->
+```{r, child='app_results_explorer_cindex_controls.Rmd'}
```
-```{r, echo=F}
-numericInput(inputId = "plot_i_max",
- label="End",
- value=NA_real_,
- width="30%")
-
-
-```
-</div> <!-- Intensity div -->
-
-#### Report
-
-<div style="display: flex-flow: row nowrap"> <!-- Control Bar -->
-```{r, echo=F}
-textInput("single_plot_fname",
- label="Filename of the single entry plot",
- value="default.pdf")
-actionButton("plot_save_single",
- label="Save single entry plot")
-textInput("report_name",
- label="Report Name",
- value="report")
-actionButton("make_report_b",
- label="Create report")
-textInput("summ_name",
- label="Summary table name",
- value="summary.csv")
-actionButton("summ_tab_b", "Save summary table")
-
-textInput("ms2_spectra_tab_name",
- label="Table of MS2 spectra",
- value="ms2_spectra_table.csv")
-actionButton("ms2_spectra_tab_b", "Save MS2 spectra table")
-```
-
-</div> <!-- Control Bar -->
-
-</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>
-<div></div>
-</div> <!-- Plots -->
-
-
-### Measurement Properties
-
-<div class="measure-prop-sec">
-
-<div class="sel-spec"> <!-- sel-spec -->
-
-#### Select Spectrum
-
-```{r, echo=F}
-selectInput("sel_parent_trace",label="Select parent", choices=character(),size=10L,selectize=F)
-```
-
-```{r, echo=F}
-selectInput("sel_spec",label="Select spectrum", choices=character(),size=10L,selectize=F)
-```
-
-```{r, echo=F}
-actionButton("cmt_changes_b",label="Commit changes")
-```
-
-</div> <!-- sel-spec -->
-
-<div class="measure-props"> <!-- measure-props -->
-
-#### Properties
-
-```{r,echo=F}
-numericInput(inputId="chg_ms1_rt",
- label="Retention time (MS1)",
- value=NA_real_)
-numericInput(inputId="chg_ms1_int",
- label="Intensity (MS1)",
- value=NA_real_)
-```
-
-```{r,echo=F}
-checkboxGroupInput(inputId="qabox",
- label="Quality Control",
- choices=QABOX_VALS)
-```
-```{r,echo=F}
-checkboxInput(inputId="chg_ms2sel",
- label="MS2 Selected",
- value=F)
-```
-</div> <!-- measure-props -->
-
-<div class="spec-tab"> <!-- spec tab -->
-
-#### Mass Spectrum
-
-```{r, echo=F}
-verbatimTextOutput("print_spec_tab")
-```
-
-</div> <!-- spec tab -->
+</div> <!-- cindex-controls -->
+</div> <!-- cindex -->
-</div> <!-- measure-prop-sec -->
<!-- ENGINE -->
diff --git a/inst/rmd/app_config_and_status.Rmd b/inst/rmd/app_config_and_status.Rmd
index 29f5fb8..8e4229b 100644
--- a/inst/rmd/app_config_and_status.Rmd
+++ b/inst/rmd/app_config_and_status.Rmd
@@ -211,6 +211,7 @@ selectInput("mf_local_database",
choices=character(0))
selectInput("mf_local_db_col_ident",
label="Select Identifiers",
+ multiple = T,
choices=character(0))
```
@@ -224,6 +225,7 @@ selectInput("mf_local_db_col_ident",
selectInput("mf_scores_intrinsic",
label="Select Scoring Types",
choices = METFRAG_INTRINSIC_SCORES,
+ multiple = T,
selected = names(METFRAG_DEFAULT_SCORES))
DT::DTOutput("mf_local_ident")
```
@@ -236,6 +238,7 @@ DT::DTOutput("mf_local_ident")
```{r, echo = F}
selectInput("mf_local_db_col_scores",
label="Select local scoring terms",
+ multiple = T,
choices=character(0))
DT::DTOutput("mf_local_db_scores")
```
diff --git a/inst/rmd/app_results_explorer_cindex.Rmd b/inst/rmd/app_results_explorer_cindex.Rmd
new file mode 100644
index 0000000..a12d057
--- /dev/null
+++ b/inst/rmd/app_results_explorer_cindex.Rmd
@@ -0,0 +1,22 @@
+### Compound Index
+
+```{r, echo=F}
+selectInput("cindex_group",label="Group",
+ choices=c(NA_character_,
+ "adduct","tag"),
+ multiple=T,
+ selected=c("adduct","tag"))
+```
+
+<div class="flex-cols"> <!-- select-grouping-labels -->
+```{r, echo=F}
+selectInput("sort1",label="Sort by ", choices=shinyscreen:::ARRANGE_CHOICES,width="15%",selected="quality")
+selectInput("sort2",label="then by ", choices=shinyscreen:::ARRANGE_CHOICES,width="15%",selected="mz")
+selectInput("sort3",label="then", choices=shinyscreen:::ARRANGE_CHOICES,width="15%")
+selectInput("sort4",label="and finally by", choices=shinyscreen:::ARRANGE_CHOICES,width="15%")
+```
+</div> <!-- select-grouping-labels --
+
+```{r, echo=F}
+DT::DTOutput("cindex")
+```
diff --git a/inst/rmd/app_results_explorer_cindex_controls.Rmd b/inst/rmd/app_results_explorer_cindex_controls.Rmd
new file mode 100644
index 0000000..4f180bf
--- /dev/null
+++ b/inst/rmd/app_results_explorer_cindex_controls.Rmd
@@ -0,0 +1,18 @@
+<div class='flex-ctrl-row'>
+```{r, echo=F}
+textInput("report_name",
+ label="Report Name",
+ value="report")
+actionButton("make_report_b",
+ label="Create report")
+textInput("summ_name",
+ label="Summary table name",
+ value="summary.csv")
+actionButton("summ_tab_b", "Save summary table")
+
+textInput("ms2_spectra_tab_name",
+ label="Table of MS2 spectra",
+ value="ms2_spectra_table.csv")
+actionButton("ms2_spectra_tab_b", "Save MS2 spectra table")
+```
+</div>
diff --git a/inst/www/custom.css b/inst/www/custom.css
index 86c38b5..1685ae5 100644
--- a/inst/www/custom.css
+++ b/inst/www/custom.css
@@ -62,8 +62,24 @@
/* test comment */
+/* Splitting items on the screen in columns. */
.flex-cols {
display: flex;
flex-direction: row nowrap;
column-gap: 1rem;
}
+
+
+/* A row of controls. */
+.flex-ctrl-row {
+ display: flex;
+ flex-direction: row wrap;
+ column-gap: 0.5rem;
+}
+
+
+/* Splitting items in horizontal layers. */
+.flex-layers {
+ display: flex;
+ flex-direction: column;
+}
--
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