diff --git a/DESCRIPTION b/DESCRIPTION
index dac0d4a65cb1f63581eedbbb55df9653caa19922..2e948c91b4632367b3b5cfb0fb926421b8220644 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -50,18 +50,12 @@ Collate:
'extraction.R'
'api.R'
'shiny-ui-base.R'
- 'shiny-ui-config.R'
- 'shiny-ui-cmpd.R'
- 'shiny-ui-sets.R'
- 'shiny-ui-gen.R'
- 'shiny-ui-top.R'
Depends:
RMassBank,
RChemMass
Imports:
tools,
scales,
- parallel,
future,
yaml,
mzR,
@@ -77,4 +71,6 @@ Imports:
shiny,
shinydashboard,
shinyFiles,
- rhandsontable
+ rhandsontable,
+ DT,
+ tcltk
diff --git a/NAMESPACE b/NAMESPACE
index 2834e651144a3bb81253eaf3e682a77d51107ebc..016758acf34db2df358d57a7b29b479932a77dec 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -12,7 +12,6 @@ export(get_fn_extr)
export(get_fn_ftab)
export(get_fn_summ)
export(grab_unit)
-export(launch)
export(list2rev)
export(load_compound_input)
export(load_data_input)
diff --git a/R/shiny-ui-cmpd.R b/R/shiny-ui-cmpd.R
deleted file mode 100644
index 7e1ed754ef82b1d347c5476a567fb36db44bc68c..0000000000000000000000000000000000000000
--- a/R/shiny-ui-cmpd.R
+++ /dev/null
@@ -1,74 +0,0 @@
-## Copyright (C) 2020 by University of Luxembourg
-
-## Licensed under the Apache License, Version 2.0 (the "License");
-## you may not use this file except in compliance with the License.
-## You may obtain a copy of the License at
-
-## http://www.apache.org/licenses/LICENSE-2.0
-
-## Unless required by applicable law or agreed to in writing, software
-## distributed under the License is distributed on an "AS IS" BASIS,
-## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-## See the License for the specific language governing permissions and
-## limitations under the License.
-
-## Commentary:
-##
-## Defines compound lists tab.
-
-
-mk_ui_cmpd <- function() {
- ## ***** Compound List Tab *****
-
- cmpdsListBox<-prim_box(title="Compounds List",
- rhandsontable::rHandsontableOutput("cmpdsCtrl"),
- width=NULL)
-
- compFileList <- shiny::verbatimTextOutput("filelist")
- ## shiny::tags$style(type="text/css", "#filelist {white-space: pre-wrap;}")
- cmpListLayout <- shiny::fluidRow(shiny::column(
- compFileList,
- cmpdsListBox,
- width = 12))
-
-
-
-
-
-
- cmpListTab <- shinydashboard::tabItem(tabName="compList",
- cmpListLayout)
-
-
- compListSideItem <- shinydashboard::menuItem(text="Compound list",
- tabName="compList",
- icon=shiny::icon("table"))
-
-
-
- return(list(tab=cmpListTab,
- side=compListSideItem))
-}
-
-server_cmpd <- function(input,output,session,rv,rf,roots) {
-
- output$filelist <- shiny::renderText({
- header <- "Compounds list generated from files:"
- cmpds <- rv$m$input$tab$cmpds
-
- files <- unique(cmpds$ORIG)
- entries <- sapply(files,function(fn) paste0('- ',fn))
- paste(c(header,entries),collapse = '\n')
- })
-
- output$cmpdsCtrl <- rhandsontable::renderRHandsontable({
- df<-rv$m$input$tab$cmpds
- out<-if (!is.null(df)) {
- df
- } else {
- EMPTY_CMPD_LIST
- }
- rhandsontable::rhandsontable(out,stretchH="all")
- })
- rv
-}
diff --git a/R/shiny-ui-config.R b/R/shiny-ui-config.R
deleted file mode 100644
index 1bcf055eba483fb1c21b0874649453a0d80677c8..0000000000000000000000000000000000000000
--- a/R/shiny-ui-config.R
+++ /dev/null
@@ -1,387 +0,0 @@
-## Copyright (C) 2020 by University of Luxembourg
-
-## Licensed under the Apache License, Version 2.0 (the "License");
-## you may not use this file except in compliance with the License.
-## You may obtain a copy of the License at
-
-## http://www.apache.org/licenses/LICENSE-2.0
-
-## Unless required by applicable law or agreed to in writing, software
-## distributed under the License is distributed on an "AS IS" BASIS,
-## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-## See the License for the specific language governing permissions and
-## limitations under the License.
-
-## Commentary:
-##
-## Defines config tab.
-
-mk_ui_config <- function() {
- browseFile <- function(title,
- buttonName,
- txtName,
- buttonTxt="Import compound list.",
- txtTxt="",
- icon="file",
- description=NULL,
- ...) {
- prim_box(title=title,
- shiny::h5(description),
- collapsible=F,...)}
-
- confImport <- prim_box(title="Import",
- shiny::includeMarkdown(system.file("ui/compounds-list-button.md",package="shinyscreen")),
- shinyFiles::shinyFilesButton("impCmpdsListB",
- label="Import compound lists.",
- title="",
- icon=shiny::icon("file"),
- multiple=T),
- shiny::includeMarkdown(system.file("ui/compound-sets-button.md",package="shinyscreen")),
- shinyFiles::shinyFilesButton("impSetIdB",
- label="Import set ID table.",
- title="",
- icon=shiny::icon("file"),
- multiple=T),
- shiny::uiOutput("fnDataFilesCtrl"),
- shinyFiles::shinyFilesButton("impDataFilesB",
- label="Import data files table.",
- title="",
- icon=shiny::icon("file"),
- multiple=F),
- width=NULL)
-
- confmzMLTags <- prim_box(title="Tags",
- shiny::textInput("tagPropInp",
- "What is a tag? (optional)",
- value=TAG_DEF_DESC),
- shiny::textInput("tagsInp",
- "Comma-delimited list of tag types.",
- value=""),
- shiny::actionButton("updTagsB",
- label = "Update tags.",
- icon=shiny::icon("bomb")),
-
- width=NULL)
-
- confState <- prim_box(title="Configuration State",
- shinyFiles::shinySaveButton(id="saveConfB",
- label="Save project configuration.",
- title="Save",
- filename = FN_CONF,
- "yaml"),
- shinyFiles::shinyFilesButton(id="restoreConfB",
- label="Restore project configuration.",
- multiple=F,
- title="Restore"),
- shinyFiles::shinyDirButton(id="switchProjB",
- label="Switch project.",
- title="Switch project.",
- icon=shiny::icon("recycle")),
- shiny::actionButton(inputId="resetConfB",
- label="Reset config (CAUTION!)",
- icon=shiny::icon("trash")),
- width=NULL)
-
-
- confmzMLtab <-prim_box(title="Raw Files in mzML Format",
- shiny::h5("Use this file table to assign adduct modes and tags to the data files."),
- shinyFiles::shinyFilesButton("mzMLB",
- label="Select mzML files",
- title="Select mzML files",
- icon=shiny::icon("files-o"),
- multiple=T),
- rhandsontable::rHandsontableOutput("mzMLtabCtrl"),
- width=NULL)
-
-
- confLayout <- shiny::fluidRow(shiny::column(confImport,
- confmzMLTags,
- confState,
- width=4),
- shiny::column(width=8,
- confmzMLtab))
-
-
- consumm <- shinydashboard::tabItem(tabName="config",
- shiny::h2(GUI_TAB_TITLE[["conf"]]),
- confLayout)
-
- confSideItem <- shinydashboard::menuItem(text=GUI_SIDE_TITLE[["conf"]],
- tabName="config",
- icon=shiny::icon("user-cog"))
-
- return(list(tab=consumm,
- side=confSideItem))
-}
-
-react_conf_f <- function(input,output,session,rv,rf) {
- ## Reactive functions.
-
-
-
- rf$get_tags_from_txt <- react_f({
- ## Tags in the text box.
- input$updTagsB
- isol(if (isTruthy(input$tagsInp)) unique(txt2tags(input$tagsInp)) else TAG_DEF)
- })
-
- rf$ctrl2mzml_df <- react_f({
- x <- tryCatch(rhandsontable::hot_to_r(input$mzMLtabCtrl),error=function(m) NULL)
- shiny::req(x)
- x
- })
-
- rf$ctrl2mzml <- react_f({
- dtable(rf$ctrl2mzml_df())
- })
-
- rf$get_all_sets <- react_f({
- m <- rf$m_input_cmpds()
- unique(m$input$tab$setid$set)})
-
- rf$m_conf <- react_f({
- m <- list()
- m$conf$project <- rv$project_path
- m$conf$compounds$cmpds <- input$cmpds #TODO multi-lists.
- m$conf$compounds$sets <- input$sets
- m$conf$data <- input$datafiles
- verify_compounds(m$conf)
- m
- })
-
- rf$m_input_cmpds <- react_f({
- m <- rf$m_conf()
- load_compound_input(m)
- })
-
- rf$m_input <- react_f({
- m <- rf$m_input_cmpds()
- mzml <- rf$ctrl2mzml()
- verify_data_df(mzml=mzml,all_sets=rf$get_all_sets())
- m$input$tab$mzml <- mzml
- m
- })
-
-
-
- rf$m <- react_f(rf$m_input())
-
- rf
-}
-
-server_conf <- function(input,output,session,rv,rf,roots) {
-
- ## ***** shinyFiles observers *****
-
-
-
- shinyFiles::shinyFileChoose(input, 'impCmpdsListB',defaultRoot=roots$def_vol(),
- defaultPath=roots$def_path(),roots=roots$get)
- shinyFiles::shinyFileChoose(input, 'impSetIdB',defaultRoot=roots$def_vol(),
- defaultPath=roots$def_path(),roots=roots$get)
- shinyFiles::shinyFileChoose(input, 'impDataFilesB',defaultRoot=roots$def_vol(),
- defaultPath=roots$def_path(),roots=roots$get)
-
-
- shinyFiles::shinyFileSave(input, 'saveConfB',defaultRoot=roots$def_vol(),
- defaultPath=roots$def_path(),roots=roots$get)
- shinyFiles::shinyFileChoose(input, 'restoreConfB',defaultRoot=roots$def_vol(),
- defaultPath=roots$def_path(),roots=roots$get)
- shinyFiles::shinyFileChoose(input, 'mzMLB',defaultRoot=roots$def_vol(),
- defaultPath=roots$def_path(),roots=roots$get)
- shinyFiles::shinyDirChoose(input, 'switchProjB',
- roots=roots$get,
- defaultRoot = "Computer",
- defaultPath = "")
-
-
- obsrv_e(input$switchProjB,{
- ## Update volumes function as needed.
- spath<-shinyFiles::parseDirPath(roots=roots$get,
- selection=input$switchProjB)
- path<- if(length(spath)>0) spath[[1]] else NA
- if (shiny::isTruthy(path)) {
- rv$project_path <- path
- }
- })
-
- obsrv_e(input$saveConfB, {
- m <- rf$m()
- fn <- shinyFiles::parseSavePath(roots=roots$get,input$saveConfB)[["datapath"]]
- validate1(fn,msg="Invalid file to save config to.")
- write_state(m,fn)
- })
-
- obsrv_e(input$restoreConfB,{
- fn <- shinyFiles::parseFilePaths(roots=roots$get,input$restoreConfB)[["datapath"]]
- assert(file.exists(fn), msg="The file is unreadable.")
- conf <- read_conf(fn)
- rv$project_path <- conf$project
- for (nm in names(conf$compounds)) {
- shiny::updateTextInput(session=session,
- inputId=nm,
- value=conf$compounds[[nm]])
- }
-
- shiny::updateTextInput(session = session,
- inputId = "datafiles",
- value = conf$data)
-
- fn <- conf$data
- assert(fn,msg = "Bad data file table path.")
- rv$work_mzml_pre <- file2tab(fn)
-
- })
-
- obsrv({
- ## update-files-on-restore
- message("update-files-on-restore")
- rv$work_mzml_pre
- m <- rf$m_input_cmpds()
- if (shiny::isTruthy(m$input$tab$setid)) {
- isol({
- all_sets <- rf$get_all_sets()
- dt <- rv$work_mzml_pre
- txt_tags <- rf$get_tags_from_txt()
- dt_tags <- unique(dt$tag)
- tags <- combine_tags(dt_tags,txt_tags)
- inp_tags <- setdiff(tags,TAG_DEF)
- shiny::updateTextInput(session = session,
- inputId = "tagsInp",
- value = inp_tags)
- rv$work_mzml <- mzml2disp(dt, sets = all_sets, tags = tags)
- })
- } else assert(m$input$tab$setid, msg = "Compounds set table not built yet.")
- })
-
- obsrv_e(input$mzMLB,{
- ## update-files-on-mzmlb
- m <- rf$m_input()
- df <- tryCatch(rhandsontable::hot_to_r(input$mzMLtabCtrl),error=function (e) NULL)
- shiny::req(df)
- fchoice<-shinyFiles::parseFilePaths(roots = roots$get,input$mzMLB)
- paths<-fchoice[["datapath"]]
- tags <- rf$get_tags_from_txt()
-
-
- df <- add_mzML_files(df,paths)
- rv$work_mzml <- df
-
- })
-
- obsrv_e(input$updTagsB,{
- message("update-tags:",Sys.time())
- df <- rf$ctrl2mzml_df()
- tags <- rf$get_tags_from_txt()
- z <- factor(as.character(df$tag), levels = tags)
- df$tag <- factor(sapply(as.character(z),function(x) if (!is.na(x)) x else TAG_DEF),levels = tags)
-
- rv$work_mzml <- df
- })
-
- obsrv_e(rv$project_path,{
- ## update-roots
- message("update-roots:",Sys.time())
- shiny::req(rv$project_path)
- dir <- normalizePath(rv$project_path,winslash = '/')
- if (roots$get()[["project"]] != dir) {
- roots$set(c("start"= roots$get()[['project']] ,
- "project" = dir))
-
- } else {
- roots$set(c("project" = dir))
- }
-
- })
-
- ## ***** Render *****
-
- ## txt_file_input(inputId = 'cmpds',
- ## input = input,
- ## label = html("The list of cmpds. Required columns: <i>ID</i>, <i>SMILES</i>, <i>Name</i> and <i>RT</i> (the last two can be empty). Remember to quote <i>SMILES</i> and <i>Name</i> entries!"),
- ## fileB = 'impCmpdsListB',
- ## volumes=roots$get) #TODO multi-lists
- ## })
- output$fnSetIdCtrl <- shiny::renderUI({
- txt_file_input(inputId = 'sets',
- input = input,
- label = html("Compounds set table. Required columns <i>ID</i> and <i>set</i>."),
- fileB = 'impSetIdB',
- volumes=roots$get)
- })
- output$fnDataFilesCtrl <- shiny::renderUI({
- m <- rf$m_conf()
- txt_file_input(inputId = 'datafiles',
- input = input,
- label = html("Data files table. Required columns <i>Files</i>, <i>tag</i>, <i>set</i> and <i>adduct</i>."),
- fileB = 'impDataFilesB',
- volumes=roots$get,
- default = file.path(m$conf$project, FN_DATA_TAB))
- })
-
- output$mzMLtabCtrl <- rhandsontable::renderRHandsontable({
- df <- rv$work_mzml
- m <- rf$m_input_cmpds()
- if (!shiny::isTruthy(df)) {
- all_sets <- rf$get_all_sets()
- txt_tags <- rf$get_tags_from_txt()
- df <- mzml2disp(EMPTY_MZML, sets = all_sets, tags = txt_tags)
- }
- rhandsontable::rhandsontable(df,stretchH="all")
- })
-
- rv
-}
-
-
-mzml2disp <- function(mzml,sets, tags) {
- ## Add factors for nicer rhandsontable output.
- df <- as.data.frame(mzml,stringsAsFactors=F)
- df$set <- factor(as.character(df$set),levels=c(SET_NA,sets))
- df$set <- factor(sapply(as.character(df$set),function (x) if (!is.na(x)) x else SET_NA),levels = c(SET_NA,sets))
- df$tag <- factor(df$tag,levels=tags)
- df$adduct <- factor(df$adduct,levels=names(DISP_ADDUCTMAP))
- df
-}
-
-disp2mzml <- function(df) {
- df$set <- as.character(df$set)
- df$adduct <- as.character(df$adduct)
- df$tag <- as.character(df$tag)
- dtable(df)
-}
-
-
-txt2tags <- function(txt) {
- ## Turns a string into tags
- x <- if (shiny::isTruthy(txt)) {
- trimws(unlist(strsplit(txt, ",")))
- } else list()
-
-
- as.list(c(TAG_DEF,x))
-}
-
-combine_tags <- function(df_tags,txt_tags) {
- unique(c(TAG_DEF,df_tags,txt_tags))
-}
-
-add_mzML_files<-function(df,paths) {
- lSet<-levels(df$set)
- if (length(lSet > 0) && !is.na(lSet)) {
-
- nR<-length(paths)
- if (nR > 0) {
- st <- nrow(df)+1
- fi <- nrow(df)+nR
- df[st:fi,'tag'] <- levels(df$tag)[[1]]
- df[st:fi,'set'] <- levels(df$set)[[1]]
- df[st:fi,'adduct'] <- levels(df$adduct)[[1]]
- df[st:fi,'Files'] <- paths
- }
- } else {
- warning("Define sets using the compound set table before trying to add files!")
-
- }
- df
-}
diff --git a/R/shiny-ui-gen.R b/R/shiny-ui-gen.R
deleted file mode 100644
index 001dd84baf6328ee4935e6d6089833f4993ab2ce..0000000000000000000000000000000000000000
--- a/R/shiny-ui-gen.R
+++ /dev/null
@@ -1,98 +0,0 @@
-## Copyright (C) 2020 by University of Luxembourg
-
-## Licensed under the Apache License, Version 2.0 (the "License");
-## you may not use this file except in compliance with the License.
-## You may obtain a copy of the License at
-
-## http://www.apache.org/licenses/LICENSE-2.0
-
-## Unless required by applicable law or agreed to in writing, software
-## distributed under the License is distributed on an "AS IS" BASIS,
-## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-## See the License for the specific language governing permissions and
-## limitations under the License.
-
-## Commentary:
-##
-## Defines gen tab.
-
-
-mk_ui_gen <- function() {
- genBoxExtract<-prim_box(title="Extract Spectra",
- num_input(inputId="genNoProc",
- label="Number of processes: ",
- value=1),
- num_input_unit(inputId="errCoarse",
- l1="Precursor m/z error (coarse) (+/-): ",
- l2="[Da]",
- value=MS1_ERR_COARSE),
- num_input_unit("errFinePPM",
- l1="Precursor m/z error (fine) (+/-): ",
- l2="[ppm]",
- value=MS1_ERR_FINE),
- num_input_unit("errEIC",
- l1="EIC m/z error (+/-): ",
- l2="[Da]",
- value=EIC_ERR),
- num_input_unit("errRTWin",
- l1="Retention time tolerance (+/-): ",
- l2="[min]",
- value=RT_EXTR_ERR),
- shiny::uiOutput("genSetSelInpCtrl"),
- shiny::actionButton(inputId="genRunB",
- label="Run!",
- icon=shiny::icon("bomb")),
- width=NULL)
-
- genBoxAutoQA<-prim_box(title="Automatic Quality Control",
- num_input("intThreshMS1",
- label="Intensity threshold (MS1): ",
- value=MS1_INT_THOLD),
- num_input("intThreshMS2",
- label="Intensity threshold (MS2): ",
- value=MS2_INT_THOLD),
- num_input("noiseFac",
- label="Signal-to-noise ratio: ",
- value=MS1_SN_FAC),
- num_input_unit("errRT",
- l1="Retention time shift tolerance (+/-): ",
- value=RT_SHIFT_ERR,
- l2="[min]"),
- shiny::actionButton(inputId="qaAutoB",
- label="Preprocess!",
- icon=shiny::icon("bomb")),
- width=NULL)
-
- genBoxProcessed<-prim_box(title="Processed Sets",
- rhandsontable::rHandsontableOutput("genTabProcCtrl"),
- width=NULL)
-
- genTab<-shinydashboard::tabItem(tabName = "gen",
- shiny::h2(GUI_TAB_TITLE[["gen"]]),
- shiny::fluidRow(shiny::column(genBoxExtract,
- width=4),
- shiny::column(genBoxProcessed,
- genBoxAutoQA,width=4)))
- genSideItem <- shinydashboard::menuItem(text=GUI_SIDE_TITLE[["gen"]],
- tabName="gen",
- icon=shiny::icon("cogs"))
-
- return(list(tab=genTab,
- side=genSideItem))
-}
-
-
-server_gen <- function(input,output,session,rv,rf,roots) {
-
-
- ## **** Observers ****
- obsrv({
- ## Run
- message("run!")
- m <- rf$m()
- m <- mk_comp_tab(m)
- message("done!")
- })
-
- rv
-}
diff --git a/R/shiny-ui-sets.R b/R/shiny-ui-sets.R
deleted file mode 100644
index 72c67400ea8380fea59c38bc6e8eba61c3991868..0000000000000000000000000000000000000000
--- a/R/shiny-ui-sets.R
+++ /dev/null
@@ -1,49 +0,0 @@
-## Copyright (C) 2020 by University of Luxembourg
-
-## Licensed under the Apache License, Version 2.0 (the "License");
-## you may not use this file except in compliance with the License.
-## You may obtain a copy of the License at
-
-## http://www.apache.org/licenses/LICENSE-2.0
-
-## Unless required by applicable law or agreed to in writing, software
-## distributed under the License is distributed on an "AS IS" BASIS,
-## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-## See the License for the specific language governing permissions and
-## limitations under the License.
-
-## Commentary:
-##
-## Defines compounds sets tab.
-
-
-mk_ui_sets <- function() {
- ## ***** Sets of compounds *****
- setIdBox<-prim_box(title="Compound Sets",
- rhandsontable::rHandsontableOutput("setIdCtrl"),
- width = NULL)
-
- setIdLayout<-shiny::fluidRow(shiny::column(setIdBox,
- width = 12))
-
- setIdTab<-shinydashboard::tabItem(tabName="setId",
- setIdLayout)
-
- setIdSideItem <- shinydashboard::menuItem(text="Compound sets",
- tabName="setId",
- icon=shiny::icon("table"))
- return(list(tab=setIdTab,
- side=setIdSideItem))
-
-}
-
-
-server_sets <- function(input,output,session,rv,rf,roots) {
- output$setIdCtrl<- rhandsontable::renderRHandsontable({
- df<-rv$m$input$tab$setid
- rhandsontable::rhandsontable(df,stretchH="all")
- })
-
- rv
-
-}
diff --git a/R/shiny-ui-top.R b/R/shiny-ui-top.R
deleted file mode 100644
index 4e7554b18d0742d8ba3c63d4528b6d0bd27356ba..0000000000000000000000000000000000000000
--- a/R/shiny-ui-top.R
+++ /dev/null
@@ -1,107 +0,0 @@
-## Copyright (C) 2020 by University of Luxembourg
-
-## Licensed under the Apache License, Version 2.0 (the "License");
-## you may not use this file except in compliance with the License.
-## You may obtain a copy of the License at
-
-## http://www.apache.org/licenses/LICENSE-2.0
-
-## Unless required by applicable law or agreed to in writing, software
-## distributed under the License is distributed on an "AS IS" BASIS,
-## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-## See the License for the specific language governing permissions and
-## limitations under the License.
-
-## Commentary:
-##
-## This is a top-level Shiny file to bind them all.
-
-mk_ui <- function (fn_style) {
- ## Top-level UI function.
-
- headerText <- "Shinyscreen"
- header <- shinydashboard::dashboardHeader(title=headerText,
- shinydashboard::dropdownMenuOutput("notify"))
-
-
- ## plugin-ui
- conf <- mk_ui_config()
- cmpd <- mk_ui_cmpd()
- sets <- mk_ui_sets()
- gen <- mk_ui_gen()
-
- sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(id='tabs',
- conf$side,
- gen$side,
- shiny::hr(),
- shiny::h5("Inputs"),
- cmpd$side,
- sets$side,
- shiny::hr()))
- body <- shinydashboard::dashboardBody(
- shiny::tags$head(shiny::tags$style(shiny::includeHTML(fn_style))),
- shinydashboard::tabItems(conf$tab,
- cmpd$tab,
- gen$tab,
- sets$tab))
-
- shinydashboard::dashboardPage(
- header,
- sidebar,
- body)
-
-}
-
-mk_shinyscreen <- function(wd=getwd(),fn_style=system.file('www/custom.css',package = 'shinyscreen')) {
- roots <- mk_roots(wd)
-
-
-
- server <- function(input,output,session) {
- ## Top-level server function.
-
- rf <- list() # Container for all
- # reactive functions.
-
- rv <- new_rv_state(project=wd) # Container for all
- # reactive values.
-
-
-
-
-
- rf <- react_conf_f(input,output,session,rv=rv,rf=rf) # Config related r. functions.
-
- ## plugin-servers
- rv <- server_conf(input,output,session,rv=rv,rf=rf,roots=roots)
- rv <- server_cmpd(input,output,session,rv=rv,rf=rf,roots=roots)
- rv <- server_sets(input,output,session,rv=rv,rf=rf,roots=roots)
- rv <- server_gen(input,output,session,rv=rv,rf=rf,roots=roots)
-
-
-
- obsrv_e(rv,{
- message(paste("rv changed at ",Sys.time()))
- })
-
- session$onSessionEnded(function () {
- stopApp()
- })
- }
- shiny::shinyApp(ui=mk_ui(fn_style=fn_style),server=server)
-
-}
-
-
-##' @export
-launch <- function(GUI=T,fn_conf="",wd=getwd(),...) {
- if (GUI) {
- app<-mk_shinyscreen(wd=wd)
- shiny::runApp(appDir = app,...)
- } else {
- if (nchar(fn_conf)==0) {
- fn_conf <- commandArgs(trailingOnly=T)[[1]]
- }
- return(run(fn_conf))
- }
-}