DESCRIPTION

 Package: shinyscreen
 Title: Pre-screening of Mass Spectrometry Data 
-Version: 1.0.1
+Version: 1.0.3
 Author: Todor Kondić
 Maintainer: Todor Kondić <todor.kondic@uni.lu>
 Authors@R: 

R/shiny-ui-base.R

@@ -655,8 +655,8 @@ mk_shinyscreen_server <- function() {
 
         rf_get_subset <- reactive({
             input$summ_subset
-            dt <- tryCatch(rhandsontable::hot_to_r(input$summ_subset),
-                           error = function(e) def_summ_subset)
+            dt <- if (NROW(input$summ_subset)==0) def_summ_subset else rhandsontable::hot_to_r(input$summ_subset)
+            
             dt[Select == shinyscreen:::SUBSET_VALS[["GOOD"]], extra := T]
             dt[Select == shinyscreen:::SUBSET_VALS[["BAD"]], extra := F]
             sdt <- dt[!is.na(extra)]
@@ -666,7 +666,8 @@ mk_shinyscreen_server <- function() {
         })
 
         rf_get_order <- reactive({
-            dt <- tryCatch(rhandsontable::hot_to_r(input$order_summ),error = function(e) def_ord_summ)
+            dt <- if (NROW(input$order_summ)==0) def_ord_summ else rhandsontable::hot_to_r(input$order_summ)
+            
             tmp <- dt[Direction == "descending",.(`Column Name`=paste0("-",`Column Name`))]
             tmp[,`Column Name`]
         })

inst/rmd/app.Rmd

@@ -403,6 +403,8 @@ actionButton(inputId = "state_file_save_b",
 
 # Extract Data and Prescreen
 
+Shinyscreen can perform spectral extraction based on the desired settings(_ppm_,_retention time window_) under the _Extraction_ tab. The extracted spectra can be subjected to prescreening based on the settings defined under the _prescreening_ tab.
+
 <details><summary>Extract spectra from data files.</summary>
 
 After Shinyscreen is configured, the compound and setid lists loaded, it
@@ -453,8 +455,67 @@ actionButton(inputId = "sortsubset_b",
 
 # Compound Explorer {.tabset}
 
+This is where the prescreening results are presented. The _Browser_ tab shows a detailed view of the MS2 data as well as the associated precursors in searchable tables. The _Viewer_ tab shows the visualisations of the EICs and the plots of the spectra.  Both kinds of outputs can be exported using portable formats. 
+
+Auto quality checks built into Shinyscreen can sometimes yield unsatisfactory results. In such cases, it is possible to manually update relevant data.
+
+Please see the respective subsections for more details.
+
+
 ## Browser
 
+<details><summary>Organise, filter and search through data.</summary>
+
+**Data Organisation**
+
+Postprocessed spectral data is presented in three tables. The first,
+always visible, table shows the list of precursors. The entries of this
+table are ordered by the following categories in order of
+significance: adduct, a data file where they were found, the ion mass
+of the precursor and then the retention time. The ordering was chosen
+because it will group together isobars.
+
+The second table shows the metadata of all the MS2 entries associated
+with the currently selected MS1 entry : the accession number (_an_, a
+chronological tag unique to the data file it stems from), the
+retention time of the signal (_RT(ms2)_), the intensity (_I(ms2)_),
+the collision energy and several quality control flags.
+
+Meaning of QC flags:
+
+- **Selected?** : Is this spectrum the _one_? Auto precscreening will
+  select the spectral entry that passed all QC checks and is the
+  closest to the MS1 peak.
+  
+- **Above threshold?** : Is the MS2 signal greater than the intensity
+  threshold specified in the _Configuration_ section?
+
+- **MS1/MS2 RT match?** : Is the MS2 within the allowed retention time
+  window around the MS1 peak? The retention time window can be change
+  in the _Configuration_ section.
+
+- **MS2 Exists?** : If no MS2 was found for the selected MS1 entry,
+  this will be unchecked.
+
+If an entry is selected from the MS2 metadata table, its mass spectrum
+is going to be shown in the third table. The spectral table is in the
+MetFrag-compatible format and can be directly pasted in the spectral
+widget on the MetFrag website. Please bear in mind that this method of
+spectral matching is for interactive purpouses only, if there are many
+spectra that should be processed with MetFrag it is much better to
+employ MetFragCL program for batch analysis. Some Shinyscreen support
+for this is already there (see _Exporting_).
+
+
+**Filtering and Searching**
+
+The filters just below the table headers can be used to limit the
+displayed data. Numerical columns accept ranges, while the content of
+the textual columns will be matched against character strings in the
+filters.
+
+</details>
+
 <div style="display: flex; vertical-align: top;margin: auto;">
 
 <div style="width: 50%;">
@@ -466,7 +527,6 @@ DT::DTOutput("compound_selector_qa")
 ```
 </div>
 
-
 <div style="width: 25%">
 ```{r, echo=F}
 DT::DTOutput("compound_ms2_table")
@@ -481,16 +541,65 @@ DT::DTOutput("compound_ms2_spectrum")
 	
 </div>
 
+<details><summary>Override auto-prescreening results (Commit manual QA).</summary>
+
+After the automatic quality control check based on the criteria
+defined in the _Prescreening_ tab is done ,it is possible to manually
+update the quality of the retrieved spectra.This can be achieved by
+double clicking on the required QA fields namely _MS1/MS2 match?_,
+_Above threshold_, _MS2 exists_ after inspecting the peaklist. Once
+the manual QA step is done, the changes can be saved by clicking the
+_Commit manual QA_ button. 
+
+</details>
+
 ```{r, echo=F}
 uiOutput("update_summ_ui")
 ```
 
+<details><summary>Export Data Browser contents.</summary>
+
+A detailed _summary table_ combining all the information from the
+_Browser_ tab can be saved in a _CSV_ file by clicking the _Export
+MS1/MS2 summary_ tab. The table can be used in combination with
+MetFragCL for batch scoring of the entries.
+
+</details>
 ```{r, echo=F}
 uiOutput("export_summ_ui")
 ```
 
+
 ## Viewer
 
+
+<details><summary> Visualize and export the plots. </summary>
+
+For any given ID, the EICs of MS1 and MS2, as well as the
+representative mass spectrum (MS2 entry with _Selected?_ checked in
+the _Data Browser_) can be visualized by selecting the corresponding
+row in the table. The plots can be zoomed-in by selecting the region
+of interest using the cursor and double click to zoom-out. It is also
+possible to plot mutiple figures by selecting different rows.
+
+Shinyscreen can export the plots in all the formats supported by R
+package _ggplot2_ (pdf, png, ...). The plot of the EICs and the mass
+spectra will be saved in _figures_ subdirectory of the project
+directory. Associated metadata for the plots are saved in _CSV_ files
+of the same basename as the plots. The plots themselves feature
+minimal legends, so please do create legends more appropriate to your
+particular use from the data in the plot _CSV_s. The plots can also be
+saved as _ggplot2_ objects by changing the extension to _.rds_. Such a
+file can be loaded into R using the `readRDS` function, and then every
+visual aspect of the plot can be manually tweaked. This can be useful
+when there is a need to comply with specific publication requirements.
+
+Button _Save this plot_ will save the currently selected plot with
+currently selected axes ranges and scaling properties. Button _Save
+all plots_ will save all the plots with default zoom/axes ranges.
+
+</details>
+
 ```{r, echo=F}
 sidebarLayout(sidebarPanel(DT::DTOutput("plot_comp_select"),
                            h5("Pointer position"),
@@ -550,8 +659,6 @@ sidebarLayout(sidebarPanel(DT::DTOutput("plot_comp_select"),
 
 ```
 
-
-
 <!-- ENGINE -->
 
 ```{r, echo = F, context = 'setup'}