diff --git a/R/api.R b/R/api.R
index 20a3fe3528ca68d5b416fdfafa2d5f97b04fec0a..03fb25793612cae6e32f94b38de18c62ef127ea7 100644
--- a/R/api.R
+++ b/R/api.R
@@ -681,14 +681,18 @@ create_plots <- function(m) {
#' `rmarkdown::run` `render_args` argument.
#' @param top_data_dir `character(1)`, a location on the server side
#' containing data directories.
-#' @param projects `character(1)`, a location on the server side containing project directories.
+#' @param metfrag_db_dir `character(1)`, a location on the server side
+#' containing MetFrag databases.
+#' @param projects `character(1)`, a location on the server side
+#' containing project directories.
#' @return Nada.
#' @author Todor Kondić
-app <- function(shiny_args=list(launch.browser=F),render_args=NULL,top_data_dir=getwd(),projects=getwd()) {
+app <- function(shiny_args=list(launch.browser=F),render_args=NULL,top_data_dir=getwd(),projects=getwd(),metfrag_db_dir="") {
dir_before <- getwd()
init <- list()
init$dir_before <- dir_before
init$top_data_dir <- norm_path(top_data_dir)
+ init$metfrag_db_dir <- metfrag_db_dir
init$projects <- norm_path(projects)
if (!dir.exists(init$top_data_dir)) stop("Data directory (top_data_dir), currently `",
init$top_data_dir,
diff --git a/inst/rmd/app.Rmd b/inst/rmd/app.Rmd
index c557b267911b5cdebd21c3e19c5f07825fa48184..b9d9ad16f0d44d714fa99a580b3772bae2dd423b 100644
--- a/inst/rmd/app.Rmd
+++ b/inst/rmd/app.Rmd
@@ -859,336 +859,6 @@ verbatimTextOutput("print_spec_tab")
</div> <!-- measure-prop-sec -->
-
-
-
-
-
-<!-- ### Compound Index -->
-
-<!-- ```{r, echo=F} -->
-
-<!-- fluidRow(column(h5("Arrange"), -->
-<!-- selectInput("sort1",label="Sort by ", choices=shinyscreen:::ARRANGE_CHOICES), -->
-<!-- selectInput("sort2",label="then by ", choices=shinyscreen:::ARRANGE_CHOICES), -->
-<!-- selectInput("sort3",label="then", choices=shinyscreen:::ARRANGE_CHOICES), -->
-<!-- selectInput("sort4",label="and finally by", choices=shinyscreen:::ARRANGE_CHOICES), -->
-<!-- width = 2), -->
-<!-- column(wellPanel(DT::DTOutput("cindex")), -->
-<!-- width = 10)) -->
-
-<!-- ``` -->
-
-
-
-
-
-<!-- ### Viewer -->
-
-<!-- ```{r, echo=F} -->
-<!-- sidebarLayout(sidebarPanel(h5("Pointer position"), -->
-<!-- textOutput("plot_hover_out"), -->
-<!-- textInput("rtrange", -->
-<!-- label = "Global RT range"), -->
-<!-- hr(), -->
-<!-- ## Not so important, TODO later. -->
-<!-- ## h5("Log scale"), -->
-<!-- ## checkboxGroupInput("plot_log", -->
-<!-- ## label=NULL, -->
-<!-- ## choices = c("MS1 EIC","MS2 EIC","MS2 Spectrum"), -->
-<!-- ## selected = character(0)), -->
-<!-- ## hr(), -->
-<!-- ## uiOutput("plot_b_ctrl"), -->
-<!-- hr(), -->
-<!-- textInput("plot_ext", -->
-<!-- label = "Plot extension", -->
-<!-- value = "pdf"), -->
-<!-- actionButton("plot_save_single", -->
-<!-- label="Save this plot"), -->
-<!-- actionButton("plot_save_all", -->
-<!-- label="Save all plots"), -->
-<!-- actionButton("make_report_b", -->
-<!-- label="Create report"), -->
-<!-- width=4), -->
-<!-- wellPanel(id = "tPanel",style = "overflow-y:scroll; max-height:80vh; background: white", -->
-<!-- plotOutput("plot_eic_ms1", -->
-<!-- hover = hoverOpts(id="plot_hover", -->
-<!-- delayType = "throttle", -->
-<!-- delay=100), -->
-<!-- dblclick = "plot_rt_click", -->
-<!-- brush = "plot_brush"), -->
-<!-- plotOutput("plot_eic_ms2", -->
-<!-- hover = hoverOpts(id="plot_hover", -->
-<!-- delayType = "throttle", -->
-<!-- delay=100), -->
-<!-- dblclick = "plot_rt_click", -->
-<!-- brush = "plot_brush"), -->
-<!-- plotOutput("plot_ms2_spec", -->
-<!-- hover = hoverOpts(id="plot_hover", -->
-<!-- delayType = "throttle", -->
-<!-- delay=100), -->
-<!-- dblclick = "plot_mz_click", -->
-<!-- brush = brushOpts(id="plot_mz_brush")) -->
-<!-- ## ,plotOutput("plot_struct") -->
-<!-- )) -->
-
-
-
-<!-- ``` -->
-
-
-<!-- ## 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%;padding-right=1.0em"> -->
-
-<!-- #### Compound selector -->
-
-<!-- ```{r, echo=F} -->
-<!-- DT::DTOutput("compound_selector") -->
-<!-- ``` -->
-
-<!-- #### MS1 quality check table -->
-
-<!-- ```{r, echo=F} -->
-<!-- DT::DTOutput("compound_selector_qa") -->
-<!-- ``` -->
-
-<!-- <div id="footer"> -->
-
-<!-- <details><summary>Narrow down entries according to the QA criteria.</summary> -->
-
-<!-- * **qa_pass** : entries that passed all checks -->
-
-<!-- * **qa_ms1_exists** : MS1 intensity is above the MS1 threshold -->
-
-<!-- * **qa_ms2_exists** : those entries for which some MS2 spectra have been found -->
-
-<!-- * **qa_ms1_above_noise** : MS1 is intense enough and above the noise level -->
-
-<!-- * **qa_ms2_good_int** : MS2 intensity is above the MS2 threshold -->
-
-<!-- * **qa_ms2_near** : MS2 spectrum is close enough to the MS1 peak -->
-
-<!-- </details> -->
-
-<!-- ```{r, echo=F} -->
-<!-- checkboxGroupInput("cmpd_sel_filter", -->
-<!-- label="Filter Results", -->
-<!-- choices = c(qa_pass="qa_pass", -->
-<!-- qa_ms2_near="qa_ms2_near", -->
-<!-- qa_ms2_good_int="qa_ms2_good_int", -->
-<!-- qa_ms2_exists="qa_ms2_exists", -->
-<!-- qa_ms1_above_noise="qa_ms1_above_noise", -->
-<!-- qa_ms1_exists="qa_ms1_exists"), -->
-<!-- inline=T, -->
-<!-- selected = character(0)) -->
-
-<!-- ``` -->
-
-<!-- </div> -->
-
-
-<!-- </div> -->
-
-
-
-<!-- <div style="width: 50%"> -->
-
-
-
-<!-- #### MS2 quality check table -->
-
-<!-- ```{r, echo=F} -->
-<!-- DT::DTOutput("compound_ms2_table") -->
-<!-- ``` -->
-
-
-
-<!-- #### MS2 spectrum -->
-
-
-<!-- ```{r, echo=F} -->
-<!-- DT::DTOutput("compound_ms2_spectrum") -->
-<!-- ``` -->
-
-<!-- </div> -->
-
-<!-- </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"), -->
-<!-- textOutput("plot_hover_out"), -->
-<!-- textInput("rtrange", -->
-<!-- label = "Global RT range"), -->
-<!-- shinyscreen::rt_input(input_rt = "plot_rt_min", -->
-<!-- input_unit = "plot_rt_min_unit", -->
-<!-- width=55, -->
-<!-- width_u=40, -->
-<!-- def_rt = "min", -->
-<!-- def_unit = "min", -->
-<!-- pref = "RT min"), -->
-
-<!-- shinyscreen::rt_input(input_rt = "plot_rt_max", -->
-<!-- input_unit = "plot_rt_max_unit", -->
-<!-- width=55, -->
-<!-- width_u=40, -->
-<!-- def_rt = "max", -->
-<!-- def_unit = "min", -->
-<!-- pref = "RT max"), -->
-<!-- hr(), -->
-<!-- ## Not so important, TODO later. -->
-<!-- ## h5("Log scale"), -->
-<!-- ## checkboxGroupInput("plot_log", -->
-<!-- ## label=NULL, -->
-<!-- ## choices = c("MS1 EIC","MS2 EIC","MS2 Spectrum"), -->
-<!-- ## selected = character(0)), -->
-<!-- ## hr(), -->
-<!-- ## uiOutput("plot_b_ctrl"), -->
-<!-- hr(), -->
-<!-- textInput("plot_ext", -->
-<!-- label = "Plot extension", -->
-<!-- value = "pdf"), -->
-<!-- actionButton("plot_save_single", -->
-<!-- label="Save this plot"), -->
-<!-- actionButton("plot_save_all", -->
-<!-- label="Save all plots"), -->
-<!-- actionButton("make_report_b", -->
-<!-- label="Create report"), -->
-<!-- width=4), -->
-
-
-
-
-
<!-- ENGINE -->
```{r, echo = F, context = 'setup'}