Skip to content
Snippets Groups Projects
Commit b8e3f9aa authored by Todor Kondić's avatar Todor Kondić
Browse files

app: Restructuring Viewer 

* app_results_explorer_cindex: New file.

* app_results_explorer_cindex_controls: New file.
parent cce8774a
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
R/api.R
+ 8
− 3
View file @ b8e3f9aa
......@@ -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$)",full.names=T)
## Copy startup files to that location.
dir.create(file.path(dir_start,'www'), showWarnings=F)
saveRDS(object = init,file=file.path(dir_start,"init.rds"))
file.copy(system.file(file.path("rmd","app.Rmd"),package = "shinyscreen"),file.path(dir_start,"app_run.Rmd"))
file.copy(system.file(file.path("rmd","app_config_and_status.Rmd"),package = "shinyscreen"),file.path(dir_start,"app_config_and_status.Rmd"))
file.copy(system.file(file.path("www","custom.css"),package = "shinyscreen"),file.path(dir_start,"www","custom.css"))
for (fn in fnms_rmd) file.copy(fn,file.path(dir_start,basename(fn)))
dir_start
}
......@@ -736,7 +741,7 @@ app <- function(projects=getwd(),
on.exit(expr=setwd(dir_before))
setwd(dir_start)
rmarkdown::run(file = "app_run.Rmd", shiny_args = shiny_args, render_args = render_args)
rmarkdown::run(file = "app.Rmd", shiny_args = shiny_args, render_args = render_args)
}
......
R/shiny-ui-base.R
+ 24
− 1
View file @ b8e3f9aa
......@@ -1213,13 +1213,36 @@ mk_shinyscreen_server <- function(projects,init) {
updateSelectInput(session=session,
inputId="mf_local_database",
choices=list.files(path=init$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
......
inst/rmd/app.Rmd
+ 8
− 203
View file @ b8e3f9aa
......@@ -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 -->
......
inst/rmd/app_config_and_status.Rmd
+ 3
− 0
View file @ b8e3f9aa
......@@ -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")
```
......
inst/rmd/app_results_explorer_cindex.Rmd 0 → 100644
+ 22
− 0
View file @ b8e3f9aa
### 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")
```
inst/rmd/app_results_explorer_cindex_controls.Rmd 0 → 100644
+ 18
− 0
View file @ b8e3f9aa
<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>
inst/www/custom.css
+ 16
− 0
View file @ b8e3f9aa
......@@ -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;
}
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment