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server.R
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server <- function (input, output, session) {
#--Importing Files--####
source('global.R', local = TRUE)
if(Sys.info()["sysname"][[1]]=="Linux" | Sys.info()["sysname"][[1]]=="Darwin") {
source("functions.R", local = TRUE)
} else {
source("functions_wsl.R", local = TRUE)
}
#--Initializing reactive values--####
current_selection <- reactiveVal()
req_tables <- reactiveValues()
all_sel_ids <- reactiveValues (dt = data.frame())
all_sel_ids_FE <- reactiveValues (dt = data.frame())
all_sel_ids_PMID <- reactiveValues (dt = data.frame())
all_sel_ids_network_STRING <- reactiveValues (dt = data.frame())
all_sel_ids_network_STITCH <- reactiveValues (dt = data.frame())
org_map <- reactiveValues(
`Homo sapiens (Human)` = 'hsapiens',
`Mus musculus (Mouse)` = 'mmusculus',
`Rattus rattus (Rat)` = "rnorvegicus",
`Bos taurus (Cow)` = "btaurus",
`Drosophila melanogaster` = "dmelanogaster",
`Ceanorhabditis elegans` = "celegans",
`Saccharomyces cerevisiae` = "scerevisiae",
`Zea mays` = "zmays",
`Arabidopsis thaliana` = "athaliana")
db_map <- reactiveValues(
`GO molecular function` = 'GO:MF',
`GO cellular component` = 'GO:CC',
`GO biological process` = 'GO:BP',
`KEGG` = 'KEGG',
`Reactome` = 'REAC',
`WikiPathways` = 'WP',
`TRANSFAC` = 'TF',
`miRTarBase` = 'MIRNA',
`Human Protein Atlas` = 'HPA',
`CORUM` = 'CORUM',
`HP` = 'HP')
species_map <- reactiveValues(
`Homo sapiens (Human)` = 9606,
`Mus musculus (Mouse)` = 10090,
`Rattus rattus (Rat)` = 10116,
`Bos taurus (Cow)` = 9913,
`Drosophila melanogaster` = 7227,
`Ceanorhabditis elegans` = 6239,
`Saccharomyces cerevisiae` = 2528333,
`Escherichia coli` = 2605620,
`Zea mays` = 381124,
`Arabidopsis thaliana` = 3702)
#--Current selection (delete this?)--####
observeEvent(input$select, {
current_selection(input$select)
})
#----Upload and convert to html multiple files (pdf, txt)----####
observeEvent(input$upload, {
cat("uploading_files...\n", file=stderr())
cat(session$token, file=stderr())
on.upload_new(input$upload, session)
removeModal()
updatePrettyCheckboxGroup(session, inputId="select",
choiceNames = file_names,
choiceValues = file_ids,
selected = file_ids
)
updatePrettyCheckboxGroup(session, inputId = 'tbl_select', choiceValues = file_ids, choiceNames = file_names, selected = file_ids)
})
#----TextAreaInput into list of files---####
observeEvent(input$addtext, {
txt.file_new(input$textinput, session)
req(input$textinput)
updateTextAreaInput(session, 'textinput', value = '', placeholder = txt_plcholder_updated)
removeModal()
updatePrettyCheckboxGroup(session, "select",
choiceNames = file_names,
choiceValues = file_ids,
selected = file_ids)
updatePrettyCheckboxGroup(session, inputId = 'tbl_select', choiceValues = file_ids, choiceNames = file_names, selected = file_ids)
})
#----TextAreaInput reset button---#
observeEvent(input$clearText, {
updateTextAreaInput(session, 'textinput', value = '', placeholder = txt_plcholder)
})
observeEvent(input$addexample, {
updateTextAreaInput(session, 'textinput', value = txt_example)
})
#----Hide panel as long as the add button has not been pushed----#
output$text_ready <- reactive({
return(isolate(input$textinput) != "" & input$addtext > 0)
})
outputOptions(output, 'text_ready', suspendWhenHidden = FALSE)
#----check if file has been uploaded----####
output$upload_ready <- reactive({
return(!is.null(input$upload))
})
outputOptions(output, 'upload_ready', suspendWhenHidden = FALSE)
#----Display the selected files in different tabpanels, annotation options and results----####
observeEvent(input$select, {
output$fileview <- renderUI({
myTabs <- lapply(input$select, function(id) {
index <- which(file_ids==id)
name <- file_names[[index]]
fpath <- file_paths[[index]]
tabPanel(title = strong(span((glue('{name}')), style='color:rgb(31, 191, 164)')),
tabBox(
id = sprintf('tabset%s', id),
tabPanel('File', icon = icon('file-alt'),
fluidRow(
div(id = sprintf('info%s', id), p('Selected entity type(s) are shown in', strong('"Entities"'), 'tab', style = 'margin-left: 8px;'), style="background-color:#fcacac;font-size:18px"),
div(id = sprintf('infonew%s', id), p(strong('New'), 'selected data are shown in', strong('"Entities"'), 'tab', style = 'margin-left: 8px;'), style="background-color:#fcacac;font-size:18px"),
actionButton(sprintf('showhide%s', id), label = NULL, icon = icon('angle-up'), size = 'sm'),
div(id = sprintf('boxpanel%s', id),
fluidRow(
column(6, pickerInput(
inputId = sprintf('typepicker%s', id),
label = 'Select entity type(s):',
choices = filterchoices,
multiple = T,
selected = filterchoices,
width = '98%',
options = list(
`actions-box` = T,
`deselect-all-text` = 'Deselect all',
`select-all-text` = 'Select all',
`none-selected-text` = 'No entity type selected',
`selected-text-format` = paste0('count > ', length(filterchoices)-1),
`count-selected-text` = 'ALL'
)
)
),
column(6,
selectizeInput(
inputId = sprintf("orgpicker%s", id),
label = "Select organism for protein annotation:",
choices = organisms$print_name,
multiple = F,
selected = "Homo sapiens (Human) [NCBI Tax. ID: 9606]", # maybe use "Homo sapiens (Human) [NCBI Tax. ID: 9606]"
width = "98%",
options = list(
placeholder = 'Select an option or start typing...'
)
)
),
column(2, offset=10,
actionLink(sprintf("org_list%s", id), "View available organisms", style="font-size:12px;text-align:right")
)
),
fluidRow(
actionBttn(inputId = sprintf('annotationbtn%s', id), label = ' Annotate ', style = 'material-flat', color="success", size = 'sm', icon = icon('highlighter')),
actionBttn(inputId = sprintf('annotreset%s', id), label = ' Reset ', style="material-flat", color="danger", size = 'sm', icon = icon('redo-alt'))
),
),
boxPlus(
width = 70,
solidHeader = T,
closable = F,
collapsible = T,
div(id=sprintf("tagging_legend%s",id), HTML('<table style="border-spacing: 0;border-collapse: collapse;width:100%">
<tr><td><b>Entity Categories:</b></td><td style="background-color:#FB8072; color:black"> Protein </td><td style="background-color: #FDB462; color:black;"> Chemical Compound </td><td style="background-color: #FFFFB3; color:black;"> Organism </td><td style="background-color: #B3DE69; color:black;"> Environment </td><td style="background-color: #8DD3C7; color:black;"> Tissue </td><td style="background-color: #80B1D3; color:black;"> Disease/Phenotype </td><td style="background-color: #D9D9D9; color:black;"> Gene Ontology term </td></tr>
</table>'), br(), style="display:none"),
tags$iframe(id = sprintf("document-%s", id), class = 'pdf_frame', src = sprintf("%s", fpath), frameborder = '0'),
enable_dropdown = T,
dropdown_icon = 'search-plus',
dropdown_menu = dropdownItemList(
style = 'background-color:rgba(0, 0, 0, 0.3);',
sliderTextInput(toString(id), '', choices = seq(from = 10, to = 200, by = 10), grid = F, selected = 100, post = '% zoom', hide_min_max = T)
),
uiOutput(sprintf("annpar-%s", id))
)
)
),
tabPanel('Entities', icon = icon('table'), style = 'width:100%;',
div(id = sprintf('infonewtab%s', id), p(strong('New'), 'selected data are shown below', style = 'margin-left: 8px;'), style="background-color:#fcacac;font-size:18px"),
boxPlus(
width = 70,
closable = F,
solidHeader = T,
collapsible = T,
pickerInput(
inputId = sprintf('filter%s', id),
label = 'Filter by Type:',
choices = filterchoices,
selected = filterchoices,
multiple = T,
options = list(
`actions-box` = T,
`deselect-all-text` = 'Deselect all',
`select-all-text` = 'Select all',
`none-selected-text` = 'No Type selected',
`selected-text-format` = paste0('count > ', length(filterchoices)-1),
`count-selected-text` = 'ALL'
)
),
DT::dataTableOutput(sprintf('tablentities%s', id)),
enable_dropdown = T,
dropdown_icon = 'download',
dropdown_menu = dropdownItemList(
style = 'background-color: thristle;',
downloadBttn(outputId = sprintf('downloadData%s', id), label = 'Download', style = 'material-flat', size = 'xs'),
p(id = sprintf('downloadtext%s', id), '(Download full or filtered table)')
),
uiOutput(sprintf("annpar-%s-ent", id))
)
)
)
)
})
do.call(tabsetPanel, myTabs)
})
})
#----Show-hide annotation options----####
observe({
lapply(input$select, function(id) {
observeEvent(input[[sprintf('showhide%s', id)]], {
show_hide_options(input[[sprintf('showhide%s', id)]],
sprintf('showhide%s', id),
sprintf('boxpanel%s', id),
session)
})
})
})
#----Show annotate buttons----####
observe({
lapply(input$select, function(id) {
observeEvent(input[[sprintf('typepicker%s', id)]], {
shinyjs::show(sprintf('annotationbtn%s', id))
shinyjs::show(sprintf('annotreset%s', id))
})
})
})
#----Rename files----####
# This event passes program execution to javascript which prompts the user for new names for chosen files
# @param "Rename Button" click
observeEvent(input$rename, {
global_positions <<- which(file_ids %in% input$select) # keeping the positions in a global variable to access after the rename
files_to_change<-c()
for(i in 1:length(global_positions))
{
files_to_change[i]<-file_names[[i]]
# session$sendCustomMessage("handler_rename", input$select)
}
session$sendCustomMessage("handler_rename", files_to_change)
})
# input$js_fileNames returns the new "renamed" file names from javascript
observeEvent(input$js_fileNames,{
for (i in 1:length(global_positions)){
if(input$js_fileNames[i] != ""){
if (file_names[global_positions[[i]][1]] != input$js_fileNames[[i]][1]){
if(is.na(match(input$js_fileNames[i], file_names))){
file_names[global_positions[i]] <<- input$js_fileNames[i]
} else session$sendCustomMessage("handler_alert", paste("Duplicate name: ", input$js_fileNames[i], " . Name didn't change.", sep=""))
}
} else session$sendCustomMessage("handler_alert", paste("Empty name found. Name didn't change.", sep=""))
}
updatePrettyCheckboxGroup(session, inputId="select",
choiceNames = file_names,
choiceValues = file_ids,
selected = NULL)
updatePrettyCheckboxGroup(session, inputId="select",
selected = file_ids)
updatePrettyCheckboxGroup(session, inputId = 'tbl_select', choiceValues = file_ids, choiceNames = file_names, selected = file_ids)
})
#----Remove selected files dialog----####
observeEvent(input$remove, {
req(input$select)
confirmSweetAlert(
session = session,
inputId = 'confirm',
type = 'warning',
title = 'Are you sure you want to delete this/these file(s)?',
btn_labels = c('No', 'Yes'),
btn_colors = c('#04B404', '#DD6B55')
)
})
#----Confirm to delete the file----####
observeEvent(input$confirm, {
if (isTRUE(input$confirm)) {
file.remove(input$select, file_names, file_ids)
updatePrettyCheckboxGroup(session, "select",
choiceNames = file_names,
choiceValues = file_ids,
selected = file_ids)
updatePrettyCheckboxGroup(session, inputId = 'tbl_select', choiceValues = file_ids, choiceNames = file_names, selected = file_ids)
}
if(length(file_names)==0)
{
print("File list is empty.")
}
},
ignoreNULL = TRUE
)
#----Run annotation with EXTRACT----####
observe({
lapply(input$select, function(id){
observeEvent(input[[sprintf('annotationbtn%s', id)]], {
if (!is.null(input[[sprintf('typepicker%s', id)]])) {
shinyjs::show(sprintf('info%s', id))
dbs=input[[sprintf('typepicker%s', id)]]
#code for the new organism input
inp_org=input[[sprintf("orgpicker%s", id)]]
if(inp_org!="")
{
org <- organisms[organisms$print_name==inp_org,]$Taxonomy_ID
}
else
{
org=""
}
var <- array(c(org, dbs))
js$table(var)
js$annotate(var)
shinyjs::show(sprintf("tagging_legend%s", id))
output[[sprintf("annpar-%s", id)]] <- renderUI({
div(
hr(),
h5(strong("Search Parameters:")),
p(strong("Search Organism: "), paste(org, collapse=", "), " | ", strong("Sources: "), paste(dbs, collapse=", ")))
})
output[[sprintf("annpar-%s-ent", id)]] <- renderUI({
div(
hr(),
h5(strong("Search Parameters:")),
p(strong("Search Organism: "), paste(org, collapse=", "), " | ", strong("Sources: "), paste(dbs, collapse=", ")))
})
}
else {
sendSweetAlert(
session = session,
type = 'warning',
title = 'Select entity type(s)'
)
}
if (input[[sprintf('annotationbtn%s', id)]] >= 2 & !is.null(input[[sprintf('typepicker%s', id)]])) {
shinyjs::show(sprintf('infonew%s', id))
shinyjs::show(sprintf('infonewtab%s', id))
shinyjs::hide(sprintf('info%s', id))
}
})
})
})
#----Reset Annotation form ---####
observe({
lapply(input$select, function(id){
observeEvent(input[[sprintf('annotreset%s', id)]], {
updatePickerInput(session, sprintf('typepicker%s', id), selected= filterchoices )
updatePickerInput(session, sprintf('orgpicker%s', id), selected= "Homo sapiens (Human) [NCBI Tax. ID: 9606]" )
index <- which(file_ids==id)
fpath <- file_paths[[index]]
runjs(sprintf("document.getElementById('document-%s').src='%s'", id, fpath))
shinyjs::hide(sprintf('infonew%s', id))
shinyjs::hide(sprintf('infonewtab%s', id))
shinyjs::hide(sprintf('info%s', id))
shinyjs::hide(sprintf("tagging_legend%s", id))
})
})
})
#----Rendering of entities datatables----####
observeEvent (input$entities, {
variable <- csv.entities(input$entities)
data <- variable[[2]]
data2 <- variable[[3]]
if(!is.null(variable)) {
#req_tables[[ toString(variable[[1]]) ]] <- data
req_tables[[ toString(variable[[1]]) ]] <- data2
react_filter <- eventReactive(input[[sprintf('filter%s', variable[[1]])]], {
return(data[data$Type %in% input[[sprintf('filter%s', variable[[1]])]],])
})
react_df <- eventReactive(input[[sprintf('tblchoose%s', variable[[1]])]], {
return(data2[data2$Type %in% input[[sprintf('tblchoose%s', variable[[1]])]],])
})
if(!is.null(variable)) {
output[[sprintf('tablentities%s', variable[[1]])]] <- DT::renderDataTable({
datatable(react_filter(), rownames = F, escape = F, selection = 'none', options = list(paging=F, scrollY="400px", scroller=T))
})
output[[sprintf('tblentities%s', variable[[1]])]] <- DT::renderDataTable({
datatable(react_df(), rownames = F, escape = F, selection = list(mode = "multiple", target = 'row'), options = list( paging=F, scrollY="300px", scroller=T, columnDefs = list(list(visible=F, targets=c(3,4))) ))
})
dt_proxy <- DT::dataTableProxy(sprintf('tblentities%s', variable[[1]]))
#---- Select / Deselect all rows---#
observeEvent(input[[sprintf('tbl_sel%s', variable[[1]])]], {
if (isTRUE(input[[sprintf('tbl_sel%s', variable[[1]])]])) {
DT::selectRows(dt_proxy, input[[sprintf('%s_rows_all', sprintf('tblentities%s', variable[[1]]))]])
}
else {
DT::selectRows(dt_proxy, NULL)
}
})
}
else {
lapply(input$select, function(id) {
sendSweetAlert(
session = session,
title = sprintf('No biological terms were found'),
)
})
}
}
else {
lapply(input$select, function(id) {
sendSweetAlert(
session = session,
title = sprintf('No biological terms were found'),
)
})
}
})
#----Download entities table----####
observe(
lapply(input$select, function(id) {
output[[sprintf('downloadData%s', id)]] <- downloadHandler(
filename = function() {
paste('Entities_', id, '.csv', sep='')
},
content = function(file) {
tbl_download <- eventReactive(input[[sprintf('filter%s', id)]], {
return(req_tables[[ toString(id) ]][req_tables[[ toString(id) ]]$Type %in% input[[sprintf('filter%s', id)]],])
})
output_d <- tbl_download()
write.csv(output_d, file)
}
)
})
)
#----Show table in combined dataset tab-----####
observe(
lapply(input[["tbl_select"]], function(id) {
observeEvent(input[[sprintf('select%s', id)]], {
data2 <- req_tables[[ toString(id) ]]
react_df <- eventReactive(input[[sprintf('tblchoose%s', id)]], {
return(data2[data2$Type %in% input[[sprintf('tblchoose%s', id)]],])
})
on.selection(input[[sprintf('%s_rows_selected', sprintf('tblentities%s', id))]], react_df(), selected_values, all_sel_ids)
choices_all <- all_sel_ids$dt
shinyjs::show(sprintf('sel_info%s', id))
shinyjs::show(sprintf('dataset_info', id))
shinyjs::hide(sprintf('dataset_null', id))
shinyjs::show("collect_FE")
shinyjs::show("collect_PMID")
shinyjs::show("collect_Pfam")
shinyjs::show("collect_STRING")
shinyjs::show("collect_STITCH")
shinyjs::show("reset_dataset")
updateTabsetPanel(session, "dataset_creator", "Dataset")
react_df_collected <- eventReactive(input$tblchoose, {
return(choices_all[choices_all$Type %in% input$tblchoose,])
})
output$collected_dataset_table <- DT::renderDataTable({
datatable(react_df_collected(), extensions = c("Buttons") ,rownames = F, colnames = c("Identifier", "Type", "Name", "Document", ""), selection = list(mode = "multiple", target = 'row'), options = list(paging=F, scrollY="400px", dom="Bfrti", scroller=T, buttons = list(list(extend='collection', buttons=c('csv', 'excel', 'pdf'), text="Download Dataset"))))
}, server = F)
})
})
)
#----Show table in FE gProfiler tab----####
observeEvent(input$collect_FE, {
all_sel_ids_FE<<-all_sel_ids
if(nrow(all_sel_ids_FE$dt)>0)
{
choices_all_FE <- all_sel_ids_FE$dt[all_sel_ids_FE$dt$Type=="Protein",]
shinyjs::hide('nodata_FE_info')
shinyjs::hide(sprintf('dataset_info', id))
shinyjs::hide(sprintf('dataset_null', id))
shinyjs::show(sprintf('analyzeinfo_FE', id))
shinyjs::show('analyze')
shinyjs::show('delete_all')
output$sel_analysis <- DT::renderDataTable({
datatable(choices_all_FE, extensions = c("Buttons"), rownames = F, colnames = c("Identifier", "Type", "Name", "Document", ""), selection = list(mode = "multiple", target = 'row'), options = list(paging=F, scrollY="400px", dom="Bfrti", scroller=T, buttons = list(list(extend='collection', buttons=c('csv', 'excel', 'pdf'), text="Download Dataset"))))
}, server=F)
}
else {
sendSweetAlert(
session = session,
title = sprintf('No terms detected in dataset.'),
)
}
})
#----Show table in FE aGOtool tab----####
observeEvent(input$collect_Pfam, {
all_sel_ids_Pfam<<-all_sel_ids
if(nrow(all_sel_ids_Pfam$dt)>0)
{
choices_all_Pfam <- all_sel_ids_Pfam$dt[all_sel_ids_Pfam$dt$Type=="Protein",]
shinyjs::hide('nodata_Pfam_info')
shinyjs::hide(sprintf('dataset_info', id))
shinyjs::hide(sprintf('dataset_null', id))
shinyjs::show(sprintf('analyzeinfo_Pfam', id))
shinyjs::show("dataset_form_Pfam")
shinyjs::show('analyze_Pfam')
shinyjs::show('delete_all_Pfam')
output$sel_analysis_Pfam <- DT::renderDataTable({
datatable(choices_all_Pfam, extensions = c("Buttons"), rownames = F, colnames = c("Identifier", "Type", "Name", "Document", ""), selection = list(mode = "multiple", target = 'row'), options = list(paging=F, scrollY="400px", dom="Bfrti", scroller=T, buttons = list(list(extend='collection', buttons=c('csv', 'excel', 'pdf'), text="Download Dataset"))))
}, server=F)
}
else {
sendSweetAlert(
session = session,
title = sprintf('No terms detected in dataset.'),
)
}
})
#----Show table in literature search tab----####
observeEvent(input$collect_PMID, {
all_sel_ids_PMID<<-all_sel_ids
if(nrow(all_sel_ids_PMID$dt)>0)
{
choices_all_PMID <- all_sel_ids_PMID$dt[all_sel_ids_PMID$dt$Type=="Protein",]
shinyjs::hide('nodata_PMID_info')
shinyjs::hide(sprintf('dataset_info', id))
shinyjs::hide(sprintf('dataset_null', id))
shinyjs::show(sprintf('analyzeinfo_PMID', id))
shinyjs::show("dataset_form_PMID")
shinyjs::show('analyze_PMID')
shinyjs::show('delete_all_PMID')
output$sel_analysis_PMID <- DT::renderDataTable({
datatable(choices_all_PMID, extensions = c("Buttons"), rownames = F, colnames = c("Identifier", "Type", "Name", "Document", ""), selection = list(mode = "multiple", target = 'row'), options = list(paging=F, scrollY="400px", dom="Bfrti", scroller=T, buttons = list(list(extend='collection', buttons=c('csv', 'excel', 'pdf'), text="Download Dataset"))))
}, server=F)
}
else {
sendSweetAlert(
session = session,
title = sprintf('No terms detected in dataset.'),
)
}
})
#----Show table in STRING Network tab----####
observeEvent(input$collect_STRING, {
all_sel_ids_network_STRING<<-all_sel_ids
if(nrow(all_sel_ids_network_STRING$dt)>0)
{
choices_all_STRING <- all_sel_ids_network_STRING$dt[all_sel_ids_network_STRING$dt$Type=="Protein",]
shinyjs::hide('nodata_STRING_info')
shinyjs::show('dataset_form_STRING')
shinyjs::hide(sprintf('dataset_info', id))
shinyjs::hide(sprintf('dataset_null', id))
shinyjs::show(sprintf('analyzeinfo_network', id))
shinyjs::show('network_string')
shinyjs::show('delete_all_network_STRING')
output$sel_analysis_network_STRING <- DT::renderDataTable({
datatable(choices_all_STRING, extensions=c("Buttons"),rownames = F, colnames = c("Identifier", "Type", "Name", "Document", ""), selection = list(mode = "multiple", target = 'row'), options = list(paging=F, dom=" Brfti",scrollY="400px", scroller=T, buttons = list(list(extend='collection', buttons=c('csv', 'excel', 'pdf'), text="Download Dataset"))))
}, server=F)
}
else
{
sendSweetAlert(
session = session,
title = sprintf('No terms detected in dataset.'),
)
}
})
#----Show table in STITCH Network tab----####
observeEvent(input$collect_STITCH, {
all_sel_ids_network_STITCH<<-all_sel_ids
if(nrow(all_sel_ids_network_STITCH$dt)>0)
{
choices_all_STITCH <- all_sel_ids_network_STITCH$dt
shinyjs::hide('nodata_STITCH_info')
shinyjs::show('dataset_form_STITCH')
shinyjs::hide(sprintf('dataset_info', id))
shinyjs::hide(sprintf('dataset_null', id))
shinyjs::show(sprintf('analyzeinfo_network_STITCH', id))
shinyjs::show('network_stitch')
shinyjs::show('delete_all_network_STITCH')
react_df_STITCH <- eventReactive(input$tblchoose_STITCH, {
return(choices_all_STITCH[choices_all_STITCH$Type %in% input$tblchoose_STITCH,])
})
output$sel_analysis_network_STITCH <- DT::renderDataTable({
datatable(react_df_STITCH(), extensions=c("Buttons"), rownames = F, colnames = c("Identifier", "Type", "Name", "Document", ""), selection = list(mode = "multiple", target = 'row'), options = list(paging=F, scrollY="400px", scroller=T, dom="Brfti", buttons = list(list(extend='collection', buttons=c('csv', 'excel', 'pdf'), text="Download Dataset"))))
}, server=F)
}
else {
sendSweetAlert(
session = session,
title = sprintf('No terms detected in dataset.'),
)
}
})
#----Delete rows in combined Dataset tab----####
observeEvent(input$collected_dataset_table_rows_selected, {
req(input$collected_dataset_table_rows_selected)
all_sel_ids$dt <- data.frame(
all_sel_ids$dt[-input$collected_dataset_table_rows_selected, ]
)
output$collected_dataset_table <- DT::renderDataTable({
datatable(all_sel_ids$dt, extensions=c("Buttons"), rownames = F, colnames = c("Identifier", "Type", "Name", "Document", ""), selection = list(mode = "multiple", target = 'row'), options = list(paging=F, scrollY="400px", scroller=T, dom="Brfti", buttons = list(list(extend='collection', buttons=c('csv', 'excel', 'pdf'), text="Download Dataset"))))
}, server=F)
})
#----Delete rows in FE gProfiler tab----####
observeEvent(input$sel_analysis_rows_selected, {
req(input$sel_analysis_rows_selected)
all_sel_ids_FE$dt <- data.frame(
all_sel_ids_FE$dt[-input$sel_analysis_rows_selected, ]
)
output$sel_analysis <- DT::renderDataTable({
datatable(all_sel_ids_FE$dt, extensions=c("Buttons"), rownames = F, colnames = c("Identifier", "Type", "Name", "Document", ""), selection = list(mode = "multiple", target = 'row'), options = list(paging=F, scrollY="400px", scroller=T, dom="Brfti", buttons = list(list(extend='collection', buttons=c('csv', 'excel', 'pdf'), text="Download Dataset"))))
}, server=F)
})
#----Delete rows in literature search tab----####
observeEvent(input$sel_analysis_PMID_rows_selected, {
req(input$sel_analysis_PMID_rows_selected)
all_sel_ids_PMID$dt <- data.frame(
all_sel_ids_PMID$dt[-input$sel_analysis_PMID_rows_selected, ]
)
output$sel_analysis_PMID <- DT::renderDataTable({
datatable(all_sel_ids_PMID$dt, rownames = F, extensions=c("Buttons"), colnames = c("Identifier", "Type", "Name", "Document", ""), selection = list(mode = "multiple", target = 'row'), options = list(paging=F, scrollY="400px", scroller=T, dom="Brfti", buttons = list(list(extend='collection', buttons=c('csv', 'excel', 'pdf'), text="Download Dataset"))))
}, server=F)
})
#----Delete rows in FE aGOtool tab----####
observeEvent(input$sel_analysis_Pfam_rows_selected, {
req(input$sel_analysis_Pfam_rows_selected)
all_sel_ids_Pfam$dt <- data.frame(
all_sel_ids_Pfam$dt[-input$sel_analysis_Pfam_rows_selected, ]
)
output$sel_analysis_Pfam <- DT::renderDataTable({
datatable(all_sel_ids_Pfam$dt, rownames = F, extensions=c("Buttons"), colnames = c("Identifier", "Type", "Name", "Document", ""), selection = list(mode = "multiple", target = 'row'), options = list(paging=F, scrollY="400px", scroller=T, dom="Brfti", buttons = list(list(extend='collection', buttons=c('csv', 'excel', 'pdf'), text="Download Dataset"))))
}, server=F)
})
#----Delete rows in STRING Network tab----####
observeEvent(input$sel_analysis_network_STRING_rows_selected, {
req(input$sel_analysis_network_STRING_rows_selected)
all_sel_ids_network_STRING$dt <- data.frame(
all_sel_ids_network_STRING$dt[-input$sel_analysis_network_STRING_rows_selected, ]
)
output$sel_analysis_network_STRING <- DT::renderDataTable({
datatable(all_sel_ids_network_STRING$dt, extensions=c("Buttons"), rownames = F, colnames = c("Identifier", "Type", "Name", "Document", ""), selection = list(mode = "multiple", target = 'row'), options = list(paging=F, scrollY="400px", scroller=T, dom="Brfti", buttons = list(list(extend='collection', buttons=c('csv', 'excel', 'pdf'), text="Download Dataset"))))
}, server=F)
})
#----Delete rows in STITCH Network tab----####
observeEvent(input$sel_analysis_network_STITCH_rows_selected, {
req(input$sel_analysis_network_STITCH_rows_selected)
all_sel_ids_network_STITCH$dt <- data.frame(
all_sel_ids_network_STITCH$dt[-input$sel_analysis_network_STITCH_rows_selected, ]
)
output$sel_analysis_network_STITCH <- DT::renderDataTable({
datatable(all_sel_ids_network_STITCH$dt, extensions=c("Buttons"), rownames = F, colnames = c("Identifier", "Type", "Name", "Document", ""), selection = list(mode = "multiple", target = 'row'), options = list(paging=F, scrollY="400px", scroller=T, dom="Brfti", buttons = list(list(extend='collection', buttons=c('csv', 'excel', 'pdf'), text="Download Dataset"))))
}, server=F)
})
#----Delete all in combined_dataset tab----####
observeEvent(input$reset_dataset, {
shinyjs::hide('analyzeinfo_FE')
shinyjs::hide('analyzeinfo_PMID')
shinyjs::hide('analyzeinfo_Pfam')
shinyjs::hide('analyzeinfo_network')
shinyjs::hide('analyzeinfo_network_STITCH')
shinyjs::show('dataset_null')
all_sel_ids$dt <- data.frame()
output$collected_dataset_table <- DT::renderDataTable({
datatable(all_sel_ids$dt, rownames = F, selection = list(mode = "multiple", target = 'row'))
})
})
#----Delete all in FE gProfiler tab----####
observeEvent(input$delete_all, {
all_sel_ids_FE$dt <- data.frame()
output$sel_analysis <- DT::renderDataTable({
datatable(all_sel_ids_FE$dt, rownames = F, selection = list(mode = "multiple", target = 'row'))
})
})
#----Delete all in literature search tab----####
observeEvent(input$delete_all_PMID, {
all_sel_ids_PMID$dt <- data.frame()
output$sel_analysis_PMID <- DT::renderDataTable({
datatable(all_sel_ids_PMID$dt, rownames = F, selection = list(mode = "multiple", target = 'row'))
})
})
#----Delete all in FE aGOtool tab----####
observeEvent(input$delete_all_Pfam, {
all_sel_ids_Pfam$dt <- data.frame()
output$sel_analysis_Pfam <- DT::renderDataTable({
datatable(all_sel_ids_Pfam$dt, rownames = F, selection = list(mode = "multiple", target = 'row'))
})
})
#----Delete all in STRING Network tab----####
observeEvent(input$delete_all_network_STRING, {
all_sel_ids_network_STRING$dt <- data.frame()
output$sel_analysis_network_STRING <- DT::renderDataTable({
datatable(all_sel_ids_network_STRING$dt, rownames = F, selection = list(mode = "multiple", target = 'row'))
})
})
#----Delete all in STITCH Network tab----####
observeEvent(input$delete_all_network_STITCH, {
all_sel_ids_network_STITCH$dt <- data.frame()
output$sel_analysis_network_STITCH <- DT::renderDataTable({
datatable(all_sel_ids_network_STITCH$dt, rownames = F, selection = list(mode = "multiple", target = 'row'))
})
})
#----ZoomIframe content----####
observe({
lapply(input$select, function(id){
observeEvent(input[[toString(id)]], {
req(input$select)
js$ZoomInIframe(input[[toString(id)]]);
})
})
})
#----------------------Tab 'Create Dataset'---------------------------####
##----Selection of entity tables----####
output$table_select <- renderUI({
prettyCheckboxGroup ( #checkboxes instead of selectinput
inputId = 'tbl_select',
label = 'Select annotated documents:',
shape = 'curve',
choiceValues = file_ids,
choiceNames = file_names,
selected = file_ids
)
})
#----Tabset panel of entity tables----####
observeEvent(input$tbl_select, {
shinyjs::hide("nodata_create_dataset")
output$tableview <- renderUI({
mytabs <- lapply(input$tbl_select, function(id) {
index <- which(file_ids==id)
name <- file_names[[index]]
tabPanel(title = strong(span((glue('{name}')), style='color:rgb(31, 191, 164)')),
id = sprintf('tabset%s', id),
style = 'width:100%;',
div(id = sprintf('selinfo%s', id), p('Select one or more', strong('entities'), 'by clicking the row(s) in the Entities table below. Check the ',
strong("Select All"), ' box to select all entities. Click the ', strong("Add to Dataset"),' button to append your selection to the ',strong("Dataset"),".",
style = 'margin-left: 8px;'), style="background-color:#e7f3fe;font-size:18px"),
div(id = sprintf('sel_info%s', id), p('Check your selected terms in the ', strong("Dataset"), "panel.", style = 'margin-left: 8px;'), style="background-color:#e7f3fe;font-size:18px"),
boxPlus(width = 70, closable = F, solidHeader = T,
pickerInput(
inputId = sprintf('tblchoose%s', id),
label = 'Filter by Type:',
choices = specifichoices,
selected = specifichoices,
multiple = T,
options = list(
`actions-box` = T,
`deselect-all-text` = 'Deselect all',
`select-all-text` = 'Select all',
`none-selected-text` = 'No Type selected'
)
),
awesomeCheckbox(inputId = sprintf('tbl_sel%s', id), label = "Select / Deselect all"),
DT::dataTableOutput(sprintf('tblentities%s', id)),
fluidRow(
column(3,offset=10, actionBttn(inputId = sprintf('select%s', id), label = 'Add to Dataset', style ="material-flat", color="primary", size = 'sm', icon = icon('plus')))
)
)
)
})
do.call(tabsetPanel, mytabs)
})
})
#------------------ANALYSIS TOOLS----------------------####
#----FE with gProfiler----####
observeEvent(input$analyze, {
showModal(modalDialog(span('Analysis in Progress, please wait...', style='color:lightseagreen'), footer = NULL, style = 'font-size:20px; text-align:center;position:absolute;top:50%;left:50%'))
#a quick POST request to see if the gProfiler service is available
gprof_check <- POST(get_base_url(), timeout(connect_timeout))
tryCatch(
expr={
gprof_check <- POST(get_base_url(), timeout(connect_timeout))
},
error = function(err) {
cat("Some connection error, probably timeout\n", file=stderr())
cat(sprintf("%s\n", err), file=stderr())
},
finally = {
if(!exists("gprof_check"))
{
gprof_check <- list() #create a "dummy" response list and set its status code to 404, to indicate error in the check below
gprof_check$status_code=404
}
}
)
cat(paste("gprof_check\n", gprof_check, sep=" ", collapse=" "), file=stderr())
if(gprof_check$status_code ==200)
{
if(input$organisms !="")
{
updateTabsetPanel(session,'all_identifiers_FE', 'Results')
req(input$organisms)
req(input$sources)
req(input$correction_method)
req(input$pvalue)
shinyjs::show('result_info')
#org = org_map[[input$organisms]] #organism
org = organisms[organisms$print_name==input$organisms,]$gprofiler_ID
srcs = unlist(input$sources) #db sources
pvalue = input$pvalue #pvalue
corr = input$correction_method #correction type
id_output_type = unlist(input$FE_id_types) # type of gene IDs for the output
identifiers <- all_sel_ids_FE$dt$Identifier #initial input identifiers
ids_init <-character(0)
for(i in 1:length(identifiers)) #remove CIDs, keep only proteins/genes
{
if(!is.na(identifiers[i]) & substring(identifiers[i],0,4) != 'CIDs')
{
ids_init <- append(ids_init, identifiers[i])
}
}
#getting all sources in a vector
dbs <- c()
for (i in srcs) {
dbs <- c(dbs, db_map[[i]])
}
#checking if ids are found, if not, nothing runs
if (length(ids_init) != 0) {
if (id_output_type=="ENSP")
{
gost_query <- ids_init
}
else
{
go_conv <-gconvert(query=ids_init, organism = org, target=id_output_type, mthreshold = Inf, filter_na = TRUE)
gost_query <- go_conv$target
if (id_output_type!="ENTREZGENE_ACC")
{
entrezid <- gconvert(ids_init, organism = org, target="ENTREZGENE_ACC", mthreshold = Inf, filter_na = TRUE)
}
else
{
entrezid<-go_conv
}
genes_init<-paste(unlist(entrezid$target), sep=" ", collapse=" ")
#print(genes_init)
post_args_kegg <- list(otherdb = "ncbi-geneid",
target="selected",
org=organisms[organisms$print_name==input$organisms,]$KEGG, # KEGG organism code, e.g. hsa
unclassified=genes_init
)
keg_req <- POST("https://www.kegg.jp/kegg-bin/id_conv", body = post_args_kegg, timeout(connect_timeout))
if(keg_req$status_code==200)
{
keg_res<-rawToChar(content(keg_req,"raw"))
#print(keg_res)
keg_res=gsub("ncbi-geneid:","",keg_res)
keg_table<-getNodeSet(htmlParse(keg_res), "//table")
keg_df<-readHTMLTable(keg_table[[1]], header=c("Entrez", "KEGG", "Name"), stringsAsFactors=F)
entrezid$KEGG<-c()
for (i in 1:nrow(entrezid))
{
if (entrezid$target[i] %in% keg_df$Entrez)
{
result<- keg_df[grepl(entrezid$target[i], keg_df$Entrez),]$KEGG
}
else
{
result<-"NULL"
}
entrezid$KEGG[i]<-result
}
}
}
#
mixed_gost <- gost(
query = gost_query,
organism = org,
user_threshold = pvalue,
correction_method = corr,
sources = dbs,
evcodes = T,
significant = T
)
print(get_base_url())
#box with input parameters used, this will appear on the top of the results panels
output$FE_parameters <- renderUI({
p(strong("Organism: "), org, " | ", strong("Sources: "), paste(dbs, collapse=", "), " | ", strong("Significance Threshold type:"), corr, " | ", strong("P-value cut-off: "), pvalue)