R/Module_LoadNetworkModule.R
In mjhelf/Mosaic: 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/Mosaic documentation built on April 28, 2022, 11:32 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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')))
)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.