R/shiny-ui-gen.R: New tab

* R/shiny-ui-gen.R(mk_ui_gen): New function.

R/shiny-ui-gen.R

+## 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))
+}