R/Module_LoadNetworkModule.R
In mjhelf/METABOseek: Metaboseek platform
Defines functions
LoadNetworkModuleUI
LoadNetworkModule
Documented in
LoadNetworkModule
LoadNetworkModuleUI
#' LoadNetworkModule
#'
#'
#' Module for loading MS2 molecular networks (graphs)
#'
#' @inherit MseekModules
#' @param layoutFunction reactive, returning the function to use for layout of the resulting graph
#'
#' @describeIn LoadNetworkModule server logic
#' @export
LoadNetworkModule <- function(input,output, session, values,
reactives = reactive({list(active = NULL)}),
layoutFunction = reactive({})){
ns <- NS(session$ns(NULL))
internalValues <- reactiveValues(numNetworks = 0)
# loadNodeTab <- callModule(UploadTableModule,'loadNodeTab',
# static = list(title = "Load node table",
# filetypes = NULL,
# format = list(header = T,
# sep = NULL,#"\t",
# quote = '"',
# stringsAsFactors = T))
# )
#
# loadEdgeTab <- callModule(UploadTableModule,'loadEdgeTab',
# static = list(title = "Load edge table",
# filetypes = NULL,
# format = list(header = T,
# sep = NULL,#"\t",
# quote = '"',
# stringsAsFactors = T))
# )
#load and reformat a network from a file
observeEvent(input$networkFileLoad$datapath,{
tryCatch({
res <- loadMseekGraph(input$networkFileLoad$datapath, layoutFunction = layoutFunction())
internalValues[[gsub("\\.[^.]*$","",input$networkFileLoad$name)]] <- res
internalValues$numNetworks <- internalValues$numNetworks + 1
removeModal()
},
error = function(e){
showNotification(paste("An error occured: ", e), duration = 0, type = "error")
}
)
})
#
# #load and reformat a network from edge and node table
# observeEvent(input$loadNetwork,{
# res <- list(tables = list(nodes = NULL,
# edges = NULL),
# graph = NULL)
#
# res$tables$nodes <- loadNodeTab$df
# res$tables$edges <- loadEdgeTab$df
#
# if(! "fixed__id" %in% colnames(res$tables$nodes)){
# res$tables$nodes$fixed__id <- res$tables$nodes[,1]
# }
#
# tryCatch({
# g1 <- graph_from_data_frame(d=res$tables$edges, vertices=res$tables$nodes, directed=F)
#
#
# #V(g1)$label <- V(g1)$parent.mass
# V(g1)$id <- seq(vcount(g1))
#
# # Removing loops from the graph:
# g1 <- igraph::simplify(g1, remove.multiple = F, remove.loops = T)
#
# #important for overview mode!
# V(g1)$subcl <- clusters(g1)$membership
#
# #make a fixed layout and add it to the graph in a way the NetworkModule will understand
# if(is.null(V(g1)$x__coord) || is.null(V(g1)$y__coord)){
# layo <- layout_components_qgraph(g1, qgraph::qgraph.layout.fruchtermanreingold)
#
# V(g1)$x__coord <- layo$layout[,1]
# V(g1)$y__coord <- layo$layout[,2]
#
# }
#
# res$graph <- g1
#
# internalValues[[gsub("\\.[^.]*$","",input$NetName)]] <- res
# internalValues$numNetworks <- internalValues$numNetworks + 1
#
# removeModal()
# },
# error = function(e){
# #print("graph not loaded")
# #print(e)
# showModal(
# modalDialog(title = "An error has occured",
# "Load a node and edge table belonging to the same network, and make sure you selected the correct Table Options (tab or comma separated?) for your input table.",
# hr(),
# p(strong("Error:")),
# p(paste(e, collapse = "\n")),
# easyClose = T
# )
# )
# }
#
# )
# })
FindMS2 <- callModule(FindMS2ScansModule, "findms2network",
values = reactiveValues(featureTables = values$featureTables,
MSData = values$MSData),
static = list(tooltip = "Make a new MS2 network from the current feature table",
label = "New MS2 network")
)
SaveNetworks <- callModule(SaveNetworkModule, "savenetworks",
reactives = reactive({list(graphname = reactives()$active,
filename = paste0("networks/",reactives()$active))}),
values = reactiveValues(Networks = internalValues,
projectData = values$projectData),
static = list(tooltip = "Save Network as a graphml file",
label = "",
allowformats = list("Metaboseek Graph (.mskg)" = ".mskg",
"graphML" = ".graphML"))
)
observeEvent(FindMS2$done,{
if(FindMS2$done){
showModal(
modalDialog(
fluidPage(
fluidRow(
p(strong("Generate an edge table for the current feature table")),
p("A network will be constructed using the available MS2 scans identified in the previous step.")
),
hr(),
if(!is.null(values$featureTables$tables[[values$featureTables$active]]$edges)){
tagList(
p(strong("An edge table exists already for this feature table. do you want to keep using it?")),
div(title = "If not selected, a new edge table will be generated using the settings below (potentially time consuming).",
checkboxInput(ns("useOldEdges"), "Use previous edge list", value = T)),
hr()
)
}else{p("")},
fluidRow(
column(2, div(title = "Use parent m/z information for networking",
checkboxInput(ns("useparentmasses"),"Use parent masses", value = T))),
column(2, div(title = "Define m/z tolerance for MS2 fragment peak matching. Peaks will be matched if they are within m/z tolerance AND/OR ppm tolerance!",
numericInput(ns("mzdiff"),"m/z tolerance", value = 0.002))),
column(2, div(title = "Define m/z tolerance for MS2 fragment peak matching in ppm. Peaks will be matched if they are within m/z tolerance AND/OR ppm tolerance!",
numericInput(ns("ppmdiff"),"ppm tolerance", value = 5))),
column(2, div(title = "Minimum number of peaks that need to match between each pair of MS2 spectra",
numericInput(ns("minpeaks"),"min. peaks", value = 6))),
column(3, div( title = "Remove noise (peaks below this reltaive intensity in a merged MS2 spectrum will be ignored)",
numericInput(ns("noise"), "Noise level in %", value = 2))),
column(1, div( title = "Search MS2 scans",
mActionButton(ns("makeNetwork"), "Proceed", red = T)))
),
fluidRow(column(2, div(title = "Remove peaks below m/z 100 before running the networking analysis",
checkboxInput(ns("removesmallfrags"),"Ignore small fragments", value = FALSE))))
),
title = "Make edges for network",
easyClose = T,
fade = F,
size = "l",
footer = modalButton("Cancel")
))
FindMS2$done <- F
}
})
output$edgeInfo <- renderUI({
if(!is.null(input$cosThresh)
&& !is.null(is.null(values$featureTables$tables[[values$featureTables$active]]$edges))){
p(paste0("With the current cutoff at ", input$cosThresh,", a network would contain ",
sum(values$featureTables$tables[[values$featureTables$active]]$edges$cosine >= input$cosThresh),
" edges."))
}
})
observeEvent(input$makeNetwork,{
tryCatch({
if(is.null(FeatureTable(values)$df$specList)
|| (!is.null(input$useOldEdges) && !input$useOldEdges)){
withProgress(message = 'Please wait!', detail = "Saving changes to Feature Table", value = 0, {
updateFT(values)
FeatureTable(values) <- getSpecList(FeatureTable(values), values$MSData$data,
merge = TRUE,
noiselevel = input$noise*0.01,
ppm = input$ppmdiff, mzdiff = input$mzdiff,
mzThreshold = if(input$removesmallfrags){100}else{NULL})
tempn <- sum(!sapply(FeatureTable(values)$df$specList,function(x){return(is.null(x) || nrow(x) == 0)}))
incProgress(0.2, detail = paste0("Calculating similarity between ", tempn, " features (",(tempn*(tempn-1))/2," comparisons)." ))
FeatureTable(values) <- FTedges(FeatureTable(values),
useParentMZs = input$useparentmasses, minpeaks = input$minpeaks, mzdiff = input$mzdiff)
if(hasError(previousStep(FeatureTable(values)))){
showNotification(paste("An error occured: ",
unlist(error(previousStep(FeatureTable(values))))),
duration = 0, type = "error")
}else{
showNotification(paste("Finished MS2 simiarity calculation"), duration = 10)
}
})
removeModal()
}
showModal(
modalDialog(
fluidPage(
fluidRow(
p(strong("Finish Network assembly")),
p("Give a name to the new network:"),
textInput(ns('NetName2'), "Network name", value = paste0("Custom_Network_", length(names(internalValues)) )),
if(length(names(internalValues)) > 1){
p(strong("Note:"),paste0("Network names that already exist (will be overriden if you use the same name): ", paste(names(internalValues)[names(internalValues) != "numNetworks"], collapse = ", ")))
}else{p("")}
),
hr(),
fluidRow(
p("Hint: You can remove edges from this network later, e.g. by setting a higher (more strict) cosine threshold. However, you have to rebuild the network if you want to use a lower cosine score threshold later."),
div( title = "Remove edges with cosine below this threshold: ",
numericInput(ns("cosThresh"), "Cosine threshold", value = 0.6))
),
fluidRow(
htmlOutput((ns("edgeInfo")))
),
fluidRow(
div( title = "Search MS2 scans",
actionButton(ns("makeNetwork2"), "Make Network"))
)
),
title = "Finish Molecular Network",
easyClose = T,
fade = F,
size = "l",
footer = modalButton("Cancel")
))
},
error = function(e){
#print("graph not loaded")
#print(e)
showModal(
modalDialog(title = "An error has occured",
"Make sure MS2 data for the current feature table is loaded into Mseek",
hr(),
p(strong("Error:")),
p(paste(e, collapse = "\n")),
easyClose = T
)
)
}
)
})
observeEvent(input$makeNetwork2,{
tryCatch({
internalValues[[gsub("\\.[^.]*$","",input$NetName2)]] <- buildMseekGraph(FeatureTable(values), cosineThreshold = input$cosThresh,
layoutFunction = layoutFunction())
internalValues$numNetworks <- internalValues$numNetworks + 1
removeModal()
},
error = function(e){
print(e)
removeModal()
showModal(
modalDialog(title = "An error has occured",
"Make sure MS2 data for the current feature table is loaded into Mseek",
hr(),
p(strong("Error:")),
p(paste(e, collapse = "\n")),
easyClose = T
)
)
}
)
})
observeEvent(input$loadNetworkModal,{
showModal(
modalDialog(
fluidPage(
fluidRow(
# column(4,
# UploadTableModuleUI(ns('loadNodeTab'))),
# column(4,
# UploadTableModuleUI(ns('loadEdgeTab'))),
# column(4,
# style = "margin-top: 45px;",
# p("Load with automatic presets"),
div(title = "Load a network file.",
fileInput(ns('networkFileLoad'),"Load network (.graphml or .mskg files only)", accept = NULL))
# fluidRow(
# column(8,
# textInput(ns('NetName'), "Network name", value = "Custom_Network_1")),
# column(4,
# style = "margin-top: 25px;",
# tags$div(title = "Load network from custom tables. Requires both a node and an edge table to be loaded.",
# actionButton(ns("loadNetwork"), "Load Network"))
# )
# )
)
),
title = "Load a network",
easyClose = T,
fade = F,
size = "l",
footer = modalButton("Cancel")
))
})
# observe({
# shinyjs::toggleState(id = "loadNetwork",condition = (!is.null(loadNodeTab$df) && !is.null(loadEdgeTab$df)))
# })
return(internalValues)
}
#' @describeIn LoadNetworkModule UI elements
#' @export
LoadNetworkModuleUI <- function(id){
ns <- NS(id)
fluidRow(
column(2,
div(title = "Load a network",
actionButton(ns("loadNetworkModal"), "", icon = icon("folder-open", lib = "font-awesome"))
)
),
column(2,
SaveNetworkModuleUI(ns("savenetworks"))
),
column(8,
FindMS2ScansModuleUI(ns('findms2network')))
)
}
mjhelf/METABOseek documentation built on April 27, 2022, 5:13 p.m.
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Defines functions LoadNetworkModuleUI LoadNetworkModule
Documented in LoadNetworkModule LoadNetworkModuleUI
#' LoadNetworkModule
#'
#'
#' Module for loading MS2 molecular networks (graphs)
#'
#' @inherit MseekModules
#' @param layoutFunction reactive, returning the function to use for layout of the resulting graph
#'
#' @describeIn LoadNetworkModule server logic
#' @export
LoadNetworkModule <- function(input,output, session, values,
reactives = reactive({list(active = NULL)}),
layoutFunction = reactive({})){
ns <- NS(session$ns(NULL))
internalValues <- reactiveValues(numNetworks = 0)
# loadNodeTab <- callModule(UploadTableModule,'loadNodeTab',
# static = list(title = "Load node table",
# filetypes = NULL,
# format = list(header = T,
# sep = NULL,#"\t",
# quote = '"',
# stringsAsFactors = T))
# )
#
# loadEdgeTab <- callModule(UploadTableModule,'loadEdgeTab',
# static = list(title = "Load edge table",
# filetypes = NULL,
# format = list(header = T,
# sep = NULL,#"\t",
# quote = '"',
# stringsAsFactors = T))
# )
#load and reformat a network from a file
observeEvent(input$networkFileLoad$datapath,{
tryCatch({
res <- loadMseekGraph(input$networkFileLoad$datapath, layoutFunction = layoutFunction())
internalValues[[gsub("\\.[^.]*$","",input$networkFileLoad$name)]] <- res
internalValues$numNetworks <- internalValues$numNetworks + 1
removeModal()
},
error = function(e){
showNotification(paste("An error occured: ", e), duration = 0, type = "error")
}
)
})
#
# #load and reformat a network from edge and node table
# observeEvent(input$loadNetwork,{
# res <- list(tables = list(nodes = NULL,
# edges = NULL),
# graph = NULL)
#
# res$tables$nodes <- loadNodeTab$df
# res$tables$edges <- loadEdgeTab$df
#
# if(! "fixed__id" %in% colnames(res$tables$nodes)){
# res$tables$nodes$fixed__id <- res$tables$nodes[,1]
# }
#
# tryCatch({
# g1 <- graph_from_data_frame(d=res$tables$edges, vertices=res$tables$nodes, directed=F)
#
#
# #V(g1)$label <- V(g1)$parent.mass
# V(g1)$id <- seq(vcount(g1))
#
# # Removing loops from the graph:
# g1 <- igraph::simplify(g1, remove.multiple = F, remove.loops = T)
#
# #important for overview mode!
# V(g1)$subcl <- clusters(g1)$membership
#
# #make a fixed layout and add it to the graph in a way the NetworkModule will understand
# if(is.null(V(g1)$x__coord) || is.null(V(g1)$y__coord)){
# layo <- layout_components_qgraph(g1, qgraph::qgraph.layout.fruchtermanreingold)
#
# V(g1)$x__coord <- layo$layout[,1]
# V(g1)$y__coord <- layo$layout[,2]
#
# }
#
# res$graph <- g1
#
# internalValues[[gsub("\\.[^.]*$","",input$NetName)]] <- res
# internalValues$numNetworks <- internalValues$numNetworks + 1
#
# removeModal()
# },
# error = function(e){
# #print("graph not loaded")
# #print(e)
# showModal(
# modalDialog(title = "An error has occured",
# "Load a node and edge table belonging to the same network, and make sure you selected the correct Table Options (tab or comma separated?) for your input table.",
# hr(),
# p(strong("Error:")),
# p(paste(e, collapse = "\n")),
# easyClose = T
# )
# )
# }
#
# )
# })
FindMS2 <- callModule(FindMS2ScansModule, "findms2network",
values = reactiveValues(featureTables = values$featureTables,
MSData = values$MSData),
static = list(tooltip = "Make a new MS2 network from the current feature table",
label = "New MS2 network")
)
SaveNetworks <- callModule(SaveNetworkModule, "savenetworks",
reactives = reactive({list(graphname = reactives()$active,
filename = paste0("networks/",reactives()$active))}),
values = reactiveValues(Networks = internalValues,
projectData = values$projectData),
static = list(tooltip = "Save Network as a graphml file",
label = "",
allowformats = list("Metaboseek Graph (.mskg)" = ".mskg",
"graphML" = ".graphML"))
)
observeEvent(FindMS2$done,{
if(FindMS2$done){
showModal(
modalDialog(
fluidPage(
fluidRow(
p(strong("Generate an edge table for the current feature table")),
p("A network will be constructed using the available MS2 scans identified in the previous step.")
),
hr(),
if(!is.null(values$featureTables$tables[[values$featureTables$active]]$edges)){
tagList(
p(strong("An edge table exists already for this feature table. do you want to keep using it?")),
div(title = "If not selected, a new edge table will be generated using the settings below (potentially time consuming).",
checkboxInput(ns("useOldEdges"), "Use previous edge list", value = T)),
hr()
)
}else{p("")},
fluidRow(
column(2, div(title = "Use parent m/z information for networking",
checkboxInput(ns("useparentmasses"),"Use parent masses", value = T))),
column(2, div(title = "Define m/z tolerance for MS2 fragment peak matching. Peaks will be matched if they are within m/z tolerance AND/OR ppm tolerance!",
numericInput(ns("mzdiff"),"m/z tolerance", value = 0.002))),
column(2, div(title = "Define m/z tolerance for MS2 fragment peak matching in ppm. Peaks will be matched if they are within m/z tolerance AND/OR ppm tolerance!",
numericInput(ns("ppmdiff"),"ppm tolerance", value = 5))),
column(2, div(title = "Minimum number of peaks that need to match between each pair of MS2 spectra",
numericInput(ns("minpeaks"),"min. peaks", value = 6))),
column(3, div( title = "Remove noise (peaks below this reltaive intensity in a merged MS2 spectrum will be ignored)",
numericInput(ns("noise"), "Noise level in %", value = 2))),
column(1, div( title = "Search MS2 scans",
mActionButton(ns("makeNetwork"), "Proceed", red = T)))
),
fluidRow(column(2, div(title = "Remove peaks below m/z 100 before running the networking analysis",
checkboxInput(ns("removesmallfrags"),"Ignore small fragments", value = FALSE))))
),
title = "Make edges for network",
easyClose = T,
fade = F,
size = "l",
footer = modalButton("Cancel")
))
FindMS2$done <- F
}
})
output$edgeInfo <- renderUI({
if(!is.null(input$cosThresh)
&& !is.null(is.null(values$featureTables$tables[[values$featureTables$active]]$edges))){
p(paste0("With the current cutoff at ", input$cosThresh,", a network would contain ",
sum(values$featureTables$tables[[values$featureTables$active]]$edges$cosine >= input$cosThresh),
" edges."))
}
})
observeEvent(input$makeNetwork,{
tryCatch({
if(is.null(FeatureTable(values)$df$specList)
|| (!is.null(input$useOldEdges) && !input$useOldEdges)){
withProgress(message = 'Please wait!', detail = "Saving changes to Feature Table", value = 0, {
updateFT(values)
FeatureTable(values) <- getSpecList(FeatureTable(values), values$MSData$data,
merge = TRUE,
noiselevel = input$noise*0.01,
ppm = input$ppmdiff, mzdiff = input$mzdiff,
mzThreshold = if(input$removesmallfrags){100}else{NULL})
tempn <- sum(!sapply(FeatureTable(values)$df$specList,function(x){return(is.null(x) || nrow(x) == 0)}))
incProgress(0.2, detail = paste0("Calculating similarity between ", tempn, " features (",(tempn*(tempn-1))/2," comparisons)." ))
FeatureTable(values) <- FTedges(FeatureTable(values),
useParentMZs = input$useparentmasses, minpeaks = input$minpeaks, mzdiff = input$mzdiff)
if(hasError(previousStep(FeatureTable(values)))){
showNotification(paste("An error occured: ",
unlist(error(previousStep(FeatureTable(values))))),
duration = 0, type = "error")
}else{
showNotification(paste("Finished MS2 simiarity calculation"), duration = 10)
}
})
removeModal()
}
showModal(
modalDialog(
fluidPage(
fluidRow(
p(strong("Finish Network assembly")),
p("Give a name to the new network:"),
textInput(ns('NetName2'), "Network name", value = paste0("Custom_Network_", length(names(internalValues)) )),
if(length(names(internalValues)) > 1){
p(strong("Note:"),paste0("Network names that already exist (will be overriden if you use the same name): ", paste(names(internalValues)[names(internalValues) != "numNetworks"], collapse = ", ")))
}else{p("")}
),
hr(),
fluidRow(
p("Hint: You can remove edges from this network later, e.g. by setting a higher (more strict) cosine threshold. However, you have to rebuild the network if you want to use a lower cosine score threshold later."),
div( title = "Remove edges with cosine below this threshold: ",
numericInput(ns("cosThresh"), "Cosine threshold", value = 0.6))
),
fluidRow(
htmlOutput((ns("edgeInfo")))
),
fluidRow(
div( title = "Search MS2 scans",
actionButton(ns("makeNetwork2"), "Make Network"))
)
),
title = "Finish Molecular Network",
easyClose = T,
fade = F,
size = "l",
footer = modalButton("Cancel")
))
},
error = function(e){
#print("graph not loaded")
#print(e)
showModal(
modalDialog(title = "An error has occured",
"Make sure MS2 data for the current feature table is loaded into Mseek",
hr(),
p(strong("Error:")),
p(paste(e, collapse = "\n")),
easyClose = T
)
)
}
)
})
observeEvent(input$makeNetwork2,{
tryCatch({
internalValues[[gsub("\\.[^.]*$","",input$NetName2)]] <- buildMseekGraph(FeatureTable(values), cosineThreshold = input$cosThresh,
layoutFunction = layoutFunction())
internalValues$numNetworks <- internalValues$numNetworks + 1
removeModal()
},
error = function(e){
print(e)
removeModal()
showModal(
modalDialog(title = "An error has occured",
"Make sure MS2 data for the current feature table is loaded into Mseek",
hr(),
p(strong("Error:")),
p(paste(e, collapse = "\n")),
easyClose = T
)
)
}
)
})
observeEvent(input$loadNetworkModal,{
showModal(
modalDialog(
fluidPage(
fluidRow(
# column(4,
# UploadTableModuleUI(ns('loadNodeTab'))),
# column(4,
# UploadTableModuleUI(ns('loadEdgeTab'))),
# column(4,
# style = "margin-top: 45px;",
# p("Load with automatic presets"),
div(title = "Load a network file.",
fileInput(ns('networkFileLoad'),"Load network (.graphml or .mskg files only)", accept = NULL))
# fluidRow(
# column(8,
# textInput(ns('NetName'), "Network name", value = "Custom_Network_1")),
# column(4,
# style = "margin-top: 25px;",
# tags$div(title = "Load network from custom tables. Requires both a node and an edge table to be loaded.",
# actionButton(ns("loadNetwork"), "Load Network"))
# )
# )
)
),
title = "Load a network",
easyClose = T,
fade = F,
size = "l",
footer = modalButton("Cancel")
))
})
# observe({
# shinyjs::toggleState(id = "loadNetwork",condition = (!is.null(loadNodeTab$df) && !is.null(loadEdgeTab$df)))
# })
return(internalValues)
}
#' @describeIn LoadNetworkModule UI elements
#' @export
LoadNetworkModuleUI <- function(id){
ns <- NS(id)
fluidRow(
column(2,
div(title = "Load a network",
actionButton(ns("loadNetworkModal"), "", icon = icon("folder-open", lib = "font-awesome"))
)
),
column(2,
SaveNetworkModuleUI(ns("savenetworks"))
),
column(8,
FindMS2ScansModuleUI(ns('findms2network')))
)
}
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