diff --git a/DESCRIPTION b/DESCRIPTION index 1209299..c8df222 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -24,7 +24,7 @@ Authors@R: c( person("Olga", "Vitek", email = "o.vitek@northeastern.edu", role = "aut")) License: Artistic-2.0 Depends: R (>= 4.2) -Imports: shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2, plotly, data.table, Hmisc, shinyFiles, +Imports: shiny (>= 1.5.0), shinyBS, shinyjs, shinybusy, dplyr, ggplot2, plotly, data.table, Hmisc, shinyFiles, MSstats,MSstatsBig, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, readxl, ggrepel, uuid, utils, stats, htmltools, methods, tidyr, grDevices, graphics, mockery, MSstatsBioNet, shinydashboard, arrow, tools, MSstatsResponse, stringr diff --git a/NAMESPACE b/NAMESPACE index 929fa6b..209d2ad 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -112,6 +112,7 @@ importFrom(shiny,img) importFrom(shiny,insertUI) importFrom(shiny,isolate) importFrom(shiny,mainPanel) +importFrom(shiny,moduleServer) importFrom(shiny,navbarMenu) importFrom(shiny,navbarPage) importFrom(shiny,nearPoints) diff --git a/R/module-visualize-network-server.R b/R/module-visualize-network-server.R index 08b267e..c6b4102 100644 --- a/R/module-visualize-network-server.R +++ b/R/module-visualize-network-server.R @@ -307,9 +307,7 @@ extractSubnetwork <- function(annotated_df, pValue, evidence, statementTypes, #' Server logic for network visualization module #' -#' @param input Shiny input object -#' @param output Shiny output object -#' @param session Shiny session object +#' @param id Module ID string #' @param parent_session Parent Shiny session #' @param dataComparison Reactive expression containing comparison data #' @@ -317,8 +315,9 @@ extractSubnetwork <- function(annotated_df, pValue, evidence, statementTypes, #' #' @importFrom MSstatsBioNet annotateProteinInfoFromIndra getSubnetworkFromIndra #' @importFrom DT renderDT datatable -#' @importFrom shiny updateSelectizeInput showNotification outputOptions -visualizeNetworkServer <- function(input, output, session, parent_session, dataComparison) { +#' @importFrom shiny moduleServer updateSelectizeInput showNotification outputOptions +visualizeNetworkServer <- function(id, parent_session, dataComparison) { + moduleServer(id, function(input, output, session) { # Output to control conditional panels output$hasValidDataComparison <- reactive({ @@ -714,4 +713,5 @@ visualizeNetworkServer <- function(input, output, session, parent_session, dataC updateLabelChoices(session, current_df) updateProteinChoices(session, current_df) }) + }) # end moduleServer } diff --git a/R/server.R b/R/server.R index 87d3b98..83ab590 100644 --- a/R/server.R +++ b/R/server.R @@ -62,7 +62,7 @@ server = function(input, output, session) { }) # visualizeNetworkServer - keep callModule if not yet refactored - callModule(visualizeNetworkServer, "network", session, data_comparison) + visualizeNetworkServer("network", parent_session = session, dataComparison = data_comparison) observe({ if(input$"loadpage-DDA_DIA" %in% c("TMT") && input$"loadpage-BIO" %in% c("PTM")) { diff --git a/man/visualizeNetworkServer.Rd b/man/visualizeNetworkServer.Rd index 07f011e..6b0a1aa 100644 --- a/man/visualizeNetworkServer.Rd +++ b/man/visualizeNetworkServer.Rd @@ -4,14 +4,10 @@ \alias{visualizeNetworkServer} \title{Server logic for network visualization module} \usage{ -visualizeNetworkServer(input, output, session, parent_session, dataComparison) +visualizeNetworkServer(id, parent_session, dataComparison) } \arguments{ -\item{input}{Shiny input object} - -\item{output}{Shiny output object} - -\item{session}{Shiny session object} +\item{id}{Module ID string} \item{parent_session}{Parent Shiny session}