R/server.R
In tanovsky/MALDImIDshiny: MALDImID
#' @importFrom shiny renderDataTable
#' @importFrom shiny insertUI
#' @importFrom shiny observeEvent
#' @importFrom shiny updateNumericInput
#' @importFrom shiny renderUI
#' @importFrom shiny showNotification
#' @importFrom shiny onSessionEnded
#' @importFrom shiny updateTabsetPanel
#' @importFrom shiny withProgress
#' @importFrom shiny removeUI
#' @importFrom shiny uiOutput
#' @importFrom shiny tagList
#' @importFrom shiny renderImage
#' @importFrom shiny validate
#' @importFrom shiny selectInput
#' @importFrom shiny plotOutput
#' @importFrom shiny HTML
#' @importFrom shiny div
#' @importFrom shiny h2
#' @importFrom shiny withTags
#' @importFrom shinyBS addTooltip
#' @importFrom shinyjs html
#' @importFrom stringr str_match
#' @importFrom tools file_ext
#' @importFrom utils read.csv
#' @importFrom shiny hideTab
#' @importFrom shiny showTab
#' @noRd
addTooltipHelper <- function(session,
id,
title,
placement = "bottom",
trigger = "hover",
options = list(delay = list(show=1000, hide=1000))) {
shinyBS::addTooltip(session = session,
id = id,
title = title,
placement = placement,
trigger = trigger
# ,
# options = options
)
}
mzValuesText_numeric <- "12\n32\n34\n45"
mzValuesText_nonNumeric <- "12\n32\n34\n45a"
ValidateAndGetMZValues <- function(textValues) {
# textValues <- mzValuesText_nonNumeric
# textValues <- mzValuesText_numeric
mzValuesVector <- as.numeric(strsplit(textValues, split = "\n")[[1]])
if ((length(mzValuesVector) == 0) | (any(is.na(mzValuesVector)))) {
return(NULL)
} else {
return(mzValuesVector)
}
}
################################################################################
# shinyServer
################################################################################
#' @noRd
MALDImIDServer <- function(input, output, session) {
shortNotificationDuration <- 3
longNotificationDuration <- 5
LABEL_NO_DATA <- "(no data)"
inputDirectory <- CreateSessionInputDirectory(session)
myData <- NULL
# notificationsTootip <<- c()
hideTab(inputId = "inTabset", target = "peptideFilepath", session = session)
hideTab(inputId = "inTabset", target = "hsilFilepath", session = session)
hideTab(inputId = "inTabset", target = "analysis", session = session)
# shinyBS::addTooltip(session = session, id = "tsvFilepathHelper",
# # bsTooltip(id = "tsvFilepathHelper",
# title = "Input a tab separated value file. It can have any extension as long as it is a tab separated",
# # placement = "right",
# placement = "bottom",
# trigger = "hover",
# # options = NULL,
# options = list(delay = list(show=1000, hide=3000)))
addTooltipHelper(session = session,
id = "conditionHelper",
title = "Input the condition to be compared")
addTooltipHelper(session = session,
id = "peptideFilepathHelper",
title = "Input a tab separated value file. It can have any extension as long as it is a tab separated.")
addTooltipHelper(session = session,
id = "hsilFilepathHelper",
title = "Input a xlsx file.")
addTooltipHelper(session = session,
id = "mzValue",
title = "Input each m/z values in a new line.\n Use '.' as decimal separator")
addTooltipHelper(session = session,
id = "Run",
title = "Run Analysis")
observeEvent(input$peptideFilepath, {
if (!is.null(input$peptideFilepath)) {
# print(inputDirectory)
file.remove(list.files(path = inputDirectory, full.names = TRUE, pattern = ".txt"))
fixUploadedFilesNames(input$peptideFilepath, inputDirectory)
myData <- read.csv(file = UploadedFilepaths(input$peptideFilepath, inputDirectory),
check.names=FALSE,
sep = "\t")
# output$importedPeptideFilepath <- renderDataTable(FixDataTable(input$peptideFilepath,
# inputDirectory,
# type = file_ext(input$peptideFilepath$datapath)),
# options = list(dom = "", searching = FALSE))
# To edit number of options just use this vector
# the 'All' option is added by default
# and the first options is selected by default
availableRowsInComboBoxOption <- c(10, 25, 50, 100)
availableRowsInComboBoxOptionsExtendedWithAll <- c(availableRowsInComboBoxOption, -1)
labelsForAvailableRowsInComboBoxOptionsExtendedWithAll <- c(
sapply(availableRowsInComboBoxOption, toString), 'All'
)
output$importedPeptideFilepath <- renderDataTable(myData,
options = list(
lengthMenu = list(availableRowsInComboBoxOptionsExtendedWithAll,
labelsForAvailableRowsInComboBoxOptionsExtendedWithAll),
pageLength = availableRowsInComboBoxOptionsExtendedWithAll[1],
autoWidth = TRUE,
scrollX = TRUE,
fillContainer = TRUE,
searching = TRUE))
}
showTab(inputId = "inTabset", target = "peptideFilepath", session = session)
hideTab(inputId = "inTabset", target = "analysis", session = session)
})
observeEvent(input$hsilFilepath, {
if (!is.null(input$hsilFilepath)) {
file.remove(list.files(path = inputDirectory, full.names = TRUE, pattern = "*.xlsx"))
fixUploadedFilesNames(input$hsilFilepath, inputDirectory)
# myData <- read.csv(file = UploadedFilepaths(input$hsilFilepath, inputDirectory),
# check.names=FALSE,
# sep = "\t")
myData <- read.xlsx(UploadedFilepaths(input$hsilFilepath, inputDirectory))
# output$importedPeptideFilepath <- renderDataTable(FixDataTable(input$hsilFilepath,
# inputDirectory,
# type = file_ext(input$hsilFilepath$datapath)),
# options = list(dom = "", searching = FALSE))
# To edit number of options just use this vector
# the 'All' option is added by default
# and the first options is selected by default
availableRowsInComboBoxOption <- c(10, 25, 50, 100)
availableRowsInComboBoxOptionsExtendedWithAll <- c(availableRowsInComboBoxOption, -1)
labelsForAvailableRowsInComboBoxOptionsExtendedWithAll <- c(
sapply(availableRowsInComboBoxOption, toString), 'All'
)
output$importedHsilFilepath <- renderDataTable(myData,
options = list(
lengthMenu = list(availableRowsInComboBoxOptionsExtendedWithAll,
labelsForAvailableRowsInComboBoxOptionsExtendedWithAll),
pageLength = availableRowsInComboBoxOptionsExtendedWithAll[1],
autoWidth = TRUE,
scrollX = TRUE,
fillContainer = TRUE,
searching = TRUE))
}
showTab(inputId = "inTabset", target = "hsilFilepath", session = session)
hideTab(inputId = "inTabset", target = "analysis", session = session)
updateTabsetPanel(session, "inTabset", selected = "hsilFilepath")
})
onSessionEnded(function() {
cat("Session Ended\n")
success <- unlink(GetSessionDirectory(session),
recursive = T)
if (success) {
print("Delete temporary folder sucessfully")
} else {
# TODO why is this not working..
# print("Failed to delete temporary folder")
# print(GetSessionDirectory(session))
}
})
observeEvent(input$Run, {
# #print("before")
# #print(notificationsTootip)
# # lapply(notificationsTootip, removeNotification)
# # notificationsTootip <<- c()
# # print("after")
# # print(notificationsTootip)
#
# if (is.null(input$tsvFilepath)) {
# notificationId <- showNotification(paste("Please upload required file"), duration = shortNotificationDuration)
# # print(notificationId)
# # print("and now notificationId!?!")
# # print(notificationId)
# # notificationsTootip <<- c(notificationsTootip, notificationId)
# # print("and now upload!?!")
# # print(notificationsTootip)
#
# return()
# }
# filepath <- UploadedFilepaths(input$tsvFilepath, inputDirectory)
# myData <- read.csv(file = filepath,
# check.names=FALSE,
# sep = "\t")
# # if ((input$outcome == LABEL_NO_DATA) & grepl("outcome", input$method)) {
# # showNotification(paste("If you select a method that to operate on the outcome, you need to select an outcome too."), duration = longNotificationDuration)
# # return()
# # }
# updateTabsetPanel(session, "inTabset", selected = "analysis")
# withProgress(message = 'Analysis in progress', {
#
# })
# # showTab(inputId = "inTabset", target = "tsvFile", session = session)
# showTab(inputId = "inTabset", target = "analysis", session = session)
# print(
# ValidateAndGetMZValues(input$mzValue)
# )
mzValues <- ValidateAndGetMZValues(input$mzValue)
if (is.null(mzValues)) {
showNotification(paste("Please insert numeric m/z values"), duration = 10)
}
# peptides <- read.csv(file = UploadedFilepaths(input$peptideFilepath, inputDirectory),
# check.names=FALSE,
# sep = "\t")
#
# hsilData <- read.csv(file = UploadedFilepaths(input$hsilFilepath, inputDirectory),
# check.names=FALSE,
# sep = "\t")
# showNotification(paste("Calculating.."), duration = 30)
results <- NULL
withProgress(message = 'Calculating..', value = 0, {
results <- GetResult(input$condition,
UploadedFilepaths(input$peptideFilepath, inputDirectory),
UploadedFilepaths(input$hsilFilepath, inputDirectory),
mzValues,
file.path(inputDirectory,'resultsMaldimyid.xlsx'))
})
# for full query
# 865.39
# 987.57
# 1905.95
# for light query
#1485.5864
# results <- GetResult('/Users/tanovsky/wip/Remy/MASSturbo/resources/peptides.txt',
# '/Users/tanovsky/wip/Remy/MASSturbo/resources/members HSIL.xlsx',
# c(865.39, 987.57, 1905, 95),
# 'resultsMaldimyid.xlsx')
availableRowsInComboBoxOption <- c(10, 25, 50, 100)
availableRowsInComboBoxOptionsExtendedWithAll <- c(availableRowsInComboBoxOption, -1)
labelsForAvailableRowsInComboBoxOptionsExtendedWithAll <- c(
sapply(availableRowsInComboBoxOption, toString), 'All'
)
output$results <- renderDataTable(results,
options = list(
lengthMenu = list(availableRowsInComboBoxOptionsExtendedWithAll,
labelsForAvailableRowsInComboBoxOptionsExtendedWithAll),
pageLength = availableRowsInComboBoxOptionsExtendedWithAll[1],
autoWidth = TRUE,
scrollX = TRUE,
fillContainer = TRUE,
searching = TRUE))
showTab(inputId = "inTabset", target = "analysis", session = session)
updateTabsetPanel(session, "inTabset", selected = "analysis")
# ./MALDImID.R peptides='/Users/tanovsky/wip/Remy/MASSturbo/resources/peptides.txt' hsilMembers='/Users/tanovsky/wip/Remy/MASSturbo/resources/members HSIL.xlsx' mzvalues='865.39, 987.57, 1905,95' output='resultsMaldimyid.xlsx'
})
output$downloadData <- myZipDownloadHandler(generatedFilename = "MALDImID",
basedir = inputDirectory,
pattern = "*.(xlsx|txt)$")
}
tanovsky/MALDImIDshiny documentation built on May 9, 2019, 2:25 a.m.
R Package Documentation
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#' @importFrom shiny renderDataTable
#' @importFrom shiny insertUI
#' @importFrom shiny observeEvent
#' @importFrom shiny updateNumericInput
#' @importFrom shiny renderUI
#' @importFrom shiny showNotification
#' @importFrom shiny onSessionEnded
#' @importFrom shiny updateTabsetPanel
#' @importFrom shiny withProgress
#' @importFrom shiny removeUI
#' @importFrom shiny uiOutput
#' @importFrom shiny tagList
#' @importFrom shiny renderImage
#' @importFrom shiny validate
#' @importFrom shiny selectInput
#' @importFrom shiny plotOutput
#' @importFrom shiny HTML
#' @importFrom shiny div
#' @importFrom shiny h2
#' @importFrom shiny withTags
#' @importFrom shinyBS addTooltip
#' @importFrom shinyjs html
#' @importFrom stringr str_match
#' @importFrom tools file_ext
#' @importFrom utils read.csv
#' @importFrom shiny hideTab
#' @importFrom shiny showTab
#' @noRd
addTooltipHelper <- function(session,
id,
title,
placement = "bottom",
trigger = "hover",
options = list(delay = list(show=1000, hide=1000))) {
shinyBS::addTooltip(session = session,
id = id,
title = title,
placement = placement,
trigger = trigger
# ,
# options = options
)
}
mzValuesText_numeric <- "12\n32\n34\n45"
mzValuesText_nonNumeric <- "12\n32\n34\n45a"
ValidateAndGetMZValues <- function(textValues) {
# textValues <- mzValuesText_nonNumeric
# textValues <- mzValuesText_numeric
mzValuesVector <- as.numeric(strsplit(textValues, split = "\n")[[1]])
if ((length(mzValuesVector) == 0) | (any(is.na(mzValuesVector)))) {
return(NULL)
} else {
return(mzValuesVector)
}
}
################################################################################
# shinyServer
################################################################################
#' @noRd
MALDImIDServer <- function(input, output, session) {
shortNotificationDuration <- 3
longNotificationDuration <- 5
LABEL_NO_DATA <- "(no data)"
inputDirectory <- CreateSessionInputDirectory(session)
myData <- NULL
# notificationsTootip <<- c()
hideTab(inputId = "inTabset", target = "peptideFilepath", session = session)
hideTab(inputId = "inTabset", target = "hsilFilepath", session = session)
hideTab(inputId = "inTabset", target = "analysis", session = session)
# shinyBS::addTooltip(session = session, id = "tsvFilepathHelper",
# # bsTooltip(id = "tsvFilepathHelper",
# title = "Input a tab separated value file. It can have any extension as long as it is a tab separated",
# # placement = "right",
# placement = "bottom",
# trigger = "hover",
# # options = NULL,
# options = list(delay = list(show=1000, hide=3000)))
addTooltipHelper(session = session,
id = "conditionHelper",
title = "Input the condition to be compared")
addTooltipHelper(session = session,
id = "peptideFilepathHelper",
title = "Input a tab separated value file. It can have any extension as long as it is a tab separated.")
addTooltipHelper(session = session,
id = "hsilFilepathHelper",
title = "Input a xlsx file.")
addTooltipHelper(session = session,
id = "mzValue",
title = "Input each m/z values in a new line.\n Use '.' as decimal separator")
addTooltipHelper(session = session,
id = "Run",
title = "Run Analysis")
observeEvent(input$peptideFilepath, {
if (!is.null(input$peptideFilepath)) {
# print(inputDirectory)
file.remove(list.files(path = inputDirectory, full.names = TRUE, pattern = ".txt"))
fixUploadedFilesNames(input$peptideFilepath, inputDirectory)
myData <- read.csv(file = UploadedFilepaths(input$peptideFilepath, inputDirectory),
check.names=FALSE,
sep = "\t")
# output$importedPeptideFilepath <- renderDataTable(FixDataTable(input$peptideFilepath,
# inputDirectory,
# type = file_ext(input$peptideFilepath$datapath)),
# options = list(dom = "", searching = FALSE))
# To edit number of options just use this vector
# the 'All' option is added by default
# and the first options is selected by default
availableRowsInComboBoxOption <- c(10, 25, 50, 100)
availableRowsInComboBoxOptionsExtendedWithAll <- c(availableRowsInComboBoxOption, -1)
labelsForAvailableRowsInComboBoxOptionsExtendedWithAll <- c(
sapply(availableRowsInComboBoxOption, toString), 'All'
)
output$importedPeptideFilepath <- renderDataTable(myData,
options = list(
lengthMenu = list(availableRowsInComboBoxOptionsExtendedWithAll,
labelsForAvailableRowsInComboBoxOptionsExtendedWithAll),
pageLength = availableRowsInComboBoxOptionsExtendedWithAll[1],
autoWidth = TRUE,
scrollX = TRUE,
fillContainer = TRUE,
searching = TRUE))
}
showTab(inputId = "inTabset", target = "peptideFilepath", session = session)
hideTab(inputId = "inTabset", target = "analysis", session = session)
})
observeEvent(input$hsilFilepath, {
if (!is.null(input$hsilFilepath)) {
file.remove(list.files(path = inputDirectory, full.names = TRUE, pattern = "*.xlsx"))
fixUploadedFilesNames(input$hsilFilepath, inputDirectory)
# myData <- read.csv(file = UploadedFilepaths(input$hsilFilepath, inputDirectory),
# check.names=FALSE,
# sep = "\t")
myData <- read.xlsx(UploadedFilepaths(input$hsilFilepath, inputDirectory))
# output$importedPeptideFilepath <- renderDataTable(FixDataTable(input$hsilFilepath,
# inputDirectory,
# type = file_ext(input$hsilFilepath$datapath)),
# options = list(dom = "", searching = FALSE))
# To edit number of options just use this vector
# the 'All' option is added by default
# and the first options is selected by default
availableRowsInComboBoxOption <- c(10, 25, 50, 100)
availableRowsInComboBoxOptionsExtendedWithAll <- c(availableRowsInComboBoxOption, -1)
labelsForAvailableRowsInComboBoxOptionsExtendedWithAll <- c(
sapply(availableRowsInComboBoxOption, toString), 'All'
)
output$importedHsilFilepath <- renderDataTable(myData,
options = list(
lengthMenu = list(availableRowsInComboBoxOptionsExtendedWithAll,
labelsForAvailableRowsInComboBoxOptionsExtendedWithAll),
pageLength = availableRowsInComboBoxOptionsExtendedWithAll[1],
autoWidth = TRUE,
scrollX = TRUE,
fillContainer = TRUE,
searching = TRUE))
}
showTab(inputId = "inTabset", target = "hsilFilepath", session = session)
hideTab(inputId = "inTabset", target = "analysis", session = session)
updateTabsetPanel(session, "inTabset", selected = "hsilFilepath")
})
onSessionEnded(function() {
cat("Session Ended\n")
success <- unlink(GetSessionDirectory(session),
recursive = T)
if (success) {
print("Delete temporary folder sucessfully")
} else {
# TODO why is this not working..
# print("Failed to delete temporary folder")
# print(GetSessionDirectory(session))
}
})
observeEvent(input$Run, {
# #print("before")
# #print(notificationsTootip)
# # lapply(notificationsTootip, removeNotification)
# # notificationsTootip <<- c()
# # print("after")
# # print(notificationsTootip)
#
# if (is.null(input$tsvFilepath)) {
# notificationId <- showNotification(paste("Please upload required file"), duration = shortNotificationDuration)
# # print(notificationId)
# # print("and now notificationId!?!")
# # print(notificationId)
# # notificationsTootip <<- c(notificationsTootip, notificationId)
# # print("and now upload!?!")
# # print(notificationsTootip)
#
# return()
# }
# filepath <- UploadedFilepaths(input$tsvFilepath, inputDirectory)
# myData <- read.csv(file = filepath,
# check.names=FALSE,
# sep = "\t")
# # if ((input$outcome == LABEL_NO_DATA) & grepl("outcome", input$method)) {
# # showNotification(paste("If you select a method that to operate on the outcome, you need to select an outcome too."), duration = longNotificationDuration)
# # return()
# # }
# updateTabsetPanel(session, "inTabset", selected = "analysis")
# withProgress(message = 'Analysis in progress', {
#
# })
# # showTab(inputId = "inTabset", target = "tsvFile", session = session)
# showTab(inputId = "inTabset", target = "analysis", session = session)
# print(
# ValidateAndGetMZValues(input$mzValue)
# )
mzValues <- ValidateAndGetMZValues(input$mzValue)
if (is.null(mzValues)) {
showNotification(paste("Please insert numeric m/z values"), duration = 10)
}
# peptides <- read.csv(file = UploadedFilepaths(input$peptideFilepath, inputDirectory),
# check.names=FALSE,
# sep = "\t")
#
# hsilData <- read.csv(file = UploadedFilepaths(input$hsilFilepath, inputDirectory),
# check.names=FALSE,
# sep = "\t")
# showNotification(paste("Calculating.."), duration = 30)
results <- NULL
withProgress(message = 'Calculating..', value = 0, {
results <- GetResult(input$condition,
UploadedFilepaths(input$peptideFilepath, inputDirectory),
UploadedFilepaths(input$hsilFilepath, inputDirectory),
mzValues,
file.path(inputDirectory,'resultsMaldimyid.xlsx'))
})
# for full query
# 865.39
# 987.57
# 1905.95
# for light query
#1485.5864
# results <- GetResult('/Users/tanovsky/wip/Remy/MASSturbo/resources/peptides.txt',
# '/Users/tanovsky/wip/Remy/MASSturbo/resources/members HSIL.xlsx',
# c(865.39, 987.57, 1905, 95),
# 'resultsMaldimyid.xlsx')
availableRowsInComboBoxOption <- c(10, 25, 50, 100)
availableRowsInComboBoxOptionsExtendedWithAll <- c(availableRowsInComboBoxOption, -1)
labelsForAvailableRowsInComboBoxOptionsExtendedWithAll <- c(
sapply(availableRowsInComboBoxOption, toString), 'All'
)
output$results <- renderDataTable(results,
options = list(
lengthMenu = list(availableRowsInComboBoxOptionsExtendedWithAll,
labelsForAvailableRowsInComboBoxOptionsExtendedWithAll),
pageLength = availableRowsInComboBoxOptionsExtendedWithAll[1],
autoWidth = TRUE,
scrollX = TRUE,
fillContainer = TRUE,
searching = TRUE))
showTab(inputId = "inTabset", target = "analysis", session = session)
updateTabsetPanel(session, "inTabset", selected = "analysis")
# ./MALDImID.R peptides='/Users/tanovsky/wip/Remy/MASSturbo/resources/peptides.txt' hsilMembers='/Users/tanovsky/wip/Remy/MASSturbo/resources/members HSIL.xlsx' mzvalues='865.39, 987.57, 1905,95' output='resultsMaldimyid.xlsx'
})
output$downloadData <- myZipDownloadHandler(generatedFilename = "MALDImID",
basedir = inputDirectory,
pattern = "*.(xlsx|txt)$")
}
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