import new dependencies for visualizing networks

[tonywu1999]

User description

DT, shinydashboard dependencies need to be imported or else everything breaks.

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PR Type

Enhancement

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Description

• Added DT and shinydashboard to the Imports section in DESCRIPTION.

• Updated NAMESPACE to include new imports from DT and shinydashboard.

• Enhanced networkUI function with new shinydashboard and DT dependencies.

• Updated RoxygenNote version in DESCRIPTION to 7.3.2.

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Changes walkthrough 📝

	Relevant files
Dependencies	DESCRIPTION Updated dependencies and RoxygenNote in `DESCRIPTION`        DESCRIPTION Added DT and shinydashboard to Imports. Updated RoxygenNote version to 7.3.2. +3/-2      NAMESPACE Added new imports for `DT` and `shinydashboard`                    NAMESPACE Added imports for DT functions like DTOutput. Added imports for shinydashboard components like dashboardPage. +12/-0
Enhancement	module-visualize-network-ui.R Enhanced `networkUI` with `shinydashboard` and `DT`            R/module-visualize-network-ui.R Added Roxygen import tags for shinydashboard and DT. Enhanced networkUI function with new dependencies. +2/-0

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🔒 No security concerns identified

⚡ Recommended focus areas for review Missing Test Coverage The networkUI function has been enhanced with new dependencies (shinydashboard and DT), but there is no indication that tests have been added or updated to validate these changes. #' @importFrom shinydashboard dashboardPage dashboardHeader dashboardSidebar dashboardBody sidebarMenu menuItem tabItems tabItem box #' @importFrom DT DTOutput networkUI <- function(id) { ns <- NS(id) tagList( shinyjs::useShinyjs(), Dependency Overhead A significant number of new imports from shinydashboard and DT have been added. It should be verified whether all these imports are necessary and if they could increase the dependency overhead unnecessarily. importFrom(DT,DTOutput) importFrom(DT,dataTableOutput) importFrom(DT,renderDataTable) importFrom(Hmisc,describe) importFrom(MSstatsBioNet,annotateProteinInfoFromIndra) importFrom(MSstatsBioNet,getSubnetworkFromIndra) importFrom(MSstatsConvert,MSstatsLogsSettings) importFrom(MSstatsPTM,FragPipetoMSstatsPTMFormat) importFrom(MSstatsPTM,MaxQtoMSstatsPTMFormat) importFrom(MSstatsPTM,PDtoMSstatsPTMFormat) importFrom(MSstatsPTM,SkylinetoMSstatsPTMFormat) importFrom(MSstatsPTM,SpectronauttoMSstatsPTMFormat) importFrom(MSstatsPTM,dataProcessPlotsPTM) importFrom(MSstatsPTM,groupComparisonPlotsPTM) importFrom(data.table,copy) importFrom(dplyr,`%>%`) importFrom(dplyr,filter) importFrom(dplyr,group_by) importFrom(dplyr,mutate) importFrom(dplyr,n) importFrom(dplyr,n_distinct) importFrom(dplyr,select) importFrom(dplyr,summarise) importFrom(dplyr,ungroup) importFrom(ggrepel,geom_text_repel) importFrom(gplots,heatmap.2) importFrom(grDevices,dev.off) importFrom(grDevices,pdf) importFrom(graphics,image) importFrom(graphics,mtext) importFrom(graphics,par) importFrom(graphics,plot.new) importFrom(htmltools,attachDependencies) importFrom(marray,maPalette) importFrom(methods,is) importFrom(methods,new) importFrom(plotly,layout) importFrom(plotly,plot_ly) importFrom(plotly,plotlyOutput) importFrom(plotly,renderPlotly) importFrom(readxl,read_excel) importFrom(shiny,HTML) importFrom(shiny,NS) importFrom(shiny,a) importFrom(shiny,actionButton) importFrom(shiny,br) importFrom(shiny,checkboxInput) importFrom(shiny,column) importFrom(shiny,conditionalPanel) importFrom(shiny,div) importFrom(shiny,downloadButton) importFrom(shiny,downloadHandler) importFrom(shiny,downloadLink) importFrom(shiny,eventReactive) importFrom(shiny,fileInput) importFrom(shiny,fluidPage) importFrom(shiny,fluidRow) importFrom(shiny,h1) importFrom(shiny,h2) importFrom(shiny,h3) importFrom(shiny,h4) importFrom(shiny,h5) importFrom(shiny,h6) importFrom(shiny,headerPanel) importFrom(shiny,hideTab) importFrom(shiny,hr) importFrom(shiny,icon) importFrom(shiny,img) importFrom(shiny,insertUI) importFrom(shiny,isolate) importFrom(shiny,mainPanel) importFrom(shiny,navbarMenu) importFrom(shiny,navbarPage) importFrom(shiny,nearPoints) importFrom(shiny,need) importFrom(shiny,numericInput) importFrom(shiny,observe) importFrom(shiny,observeEvent) importFrom(shiny,p) importFrom(shiny,plotOutput) importFrom(shiny,radioButtons) importFrom(shiny,reactive) importFrom(shiny,reactiveFileReader) importFrom(shiny,reactiveValues) importFrom(shiny,renderPlot) importFrom(shiny,renderPrint) importFrom(shiny,renderTable) importFrom(shiny,renderText) importFrom(shiny,renderUI) importFrom(shiny,req) importFrom(shiny,selectInput) importFrom(shiny,selectizeInput) importFrom(shiny,shinyApp) importFrom(shiny,shinyUI) importFrom(shiny,showTab) importFrom(shiny,sidebarLayout) importFrom(shiny,sidebarPanel) importFrom(shiny,sliderInput) importFrom(shiny,span) importFrom(shiny,tabPanel) importFrom(shiny,tableOutput) importFrom(shiny,tabsetPanel) importFrom(shiny,tagList) importFrom(shiny,tags) importFrom(shiny,textInput) importFrom(shiny,textOutput) importFrom(shiny,titlePanel) importFrom(shiny,uiOutput) importFrom(shiny,updateSelectInput) importFrom(shiny,updateTabsetPanel) importFrom(shiny,validate) importFrom(shiny,verbatimTextOutput) importFrom(shiny,wellPanel) importFrom(shinyBS,bsTooltip) importFrom(shinyBS,tipify) importFrom(shinybusy,remove_modal_progress) importFrom(shinybusy,remove_modal_spinner) importFrom(shinybusy,show_modal_progress_line) importFrom(shinybusy,show_modal_spinner) importFrom(shinybusy,update_modal_progress) importFrom(shinybusy,use_busy_spinner) importFrom(shinydashboard,box) importFrom(shinydashboard,dashboardBody) importFrom(shinydashboard,dashboardHeader) importFrom(shinydashboard,dashboardPage) importFrom(shinydashboard,dashboardSidebar) importFrom(shinydashboard,menuItem) importFrom(shinydashboard,sidebarMenu) importFrom(shinydashboard,tabItem) importFrom(shinydashboard,tabItems)

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