inst/shiny/app.R
In broadinstitute/infercnvApp: An R shiny app to Infer Copy Number Variation from Single-Cell RNA-Seq Data
#!/usr/bin/env Rscript
################### Load the libraries and source modules ##########################
# Load libraries
library(shiny)
# source needed modules
source("createObject.R")
source("homePage.R")
source("runInfercnv.R")
source("mainAnalysisOutputTab.R")
source("bayesianAnalysisTab.R")
source("hmmAnalysisOutputTab.R")
source("adjustByProbThreshold.R")
source("diagnosticPlotTab.R")
source("medianFilterTab.R")
source("cnvCellProbsTab.R")
options(error = function() traceback(2))
options(shiny.reactlog=TRUE)
futile.logger::flog.appender(futile.logger::appender.console())
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Preform when the app is closed
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Remove the PDF files from the www folder when the app is closed
onStop(function(){
pdf_files <- list.files(path = "www",
pattern = "*.pdf",
all.files = FALSE,
full.names = TRUE)
unlink(pdf_files)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
######################## Set up the User Interface (UI) #########################
#' This is the user-interface definition of a Shiny web application
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ui <- tags$div(
class = "navbarMain",
shinyalert::useShinyalert(),
navbarPage(title = paste0("Infercnv-",packageVersion("infercnv")),
#----------- Set up the header and themes --------------
collapsible = FALSE,
inverse = TRUE,
windowTitle = "Infercnv",
position = "fixed-top",
############################# Home Tab #############################
tabPanel(title = shiny::HTML('<i class="fa fa-home fa-fw" aria-hidden="true"></i> Home'),
homePageUI("HomePage"),
),
############################# Upload and settings TAB ########################################
tabPanel(title = shiny::HTML('<i class="fa fa-file-text-o" aria-hidden="true"></i> Upload Files And Settings'),
#-------------------------- Create the infercnv Object --------------------------
createObjectInputsUI("create_object"),
# Add the action button
actionButton(inputId = "create_obj",
label = "Upload Data Files",
icon = icon(name = "cloud-upload-alt", lib = "font-awesome"),
width = '100%',
style="color: #fff; background-color: #68D77B"),
#-------------------------- Run Analysis --------------------------
tags$br(),
tags$hr(style="border-color: black;"),
tags$br(),
titlePanel(
tags$h1("Step 2: Settings And Run Analysis",
align = "center",
style = "background-color: #afc9eb;
color: black;
margin: -20px;
padding: 50px")
),
tags$br(),tags$br(),
# Run the module for infercnv analysis
runInfercnvUI("running_infercnv"),
# Create the button for running the infercnv analysis
actionButton(inputId = "run_infercnv",
label = " Run Infercnv",
icon = icon("refresh", lib = "font-awesome"),
width = '100%',
style="color: #fff; background-color: #68D77B"),
tags$br(),tags$br(),tags$br(),
# Button to clear the output folder
actionButton(inputId = "clear_output",
label = "Clear Output",
icon = icon("refresh", lib = "font-awesome"),
width = '100%',
style="color: #fff; background-color: red"),
tags$br(),tags$br(),tags$br(),
),
############################# Analysis Output tab #############################
tabPanel(title = shiny::HTML('<i class="fa fa-bar-chart" aria-hidden="true"></i> Analysis Output'),
tags$head(includeCSS("www/infercnv.style.css")),
tags$div(class = "navbarPageHome",
navbarPage(
title = "",
#-------------------------- Main Analysis Tab --------------------------
navbarMenu(
title = "Main Analysis Output",
tabPanel(title = "Main Analysis Output",
mainAnalysisTabUI("output_main_analysis")
),
tabPanel(title = "Median Filter Output",
medianFilterUI("median_filter_output")
)
),
#-------------------------- HMM Analysis Tab --------------------------
tabPanel(title = "HMM Analysis Output",
hmmAnalysisUI("output_hmm_analysis")
),
#-------------------------- Bayesian Analysis Tab --------------------------
navbarMenu(
title = "Bayesian Analysis Output",
tabPanel(title = "Bayesian Analysis Plots",
bayesianAnalysisUI("output_bayesian_analysis")
),
tabPanel(title = "Probability Plots",
cnvCellProbsUI("cnv_cell_probs")
)
),
#-------------------------- Dytnamic Analysis Tab --------------------------
tabPanel(title = "Dynamic Plots",
adjustByProbThresholdUI("output_dynamic_analysis")
),
#-------------------------- Supplemental Tab --------------------------
navbarMenu(
title = "Supplemental",
tabPanel(title = "Diagnostic Plots",
diagnosticPlotsUI("diagploting")
)
)
)
)
),
#Add a icon to the right of the navbar
tags$script(shiny::HTML("var header = $('.navbarMain > .navbar > .container-fluid');
header.append('<div style=\"float:right\"><i class=\"fa fa-dna fa-fw\" aria-hidden=\"true\" style=\"float:right; width:33px;height:41px;padding-top:20px;color:white\"></i> `</div>');
console.log(header)")
)
)
)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
######################## Set up the Server #########################
# This is the server logic of a Shiny web application. You can run the
# application by clicking 'Run App' above.
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
server <- function(input,
output,session){
# set the max upload size 1GB
options(shiny.maxRequestSize=10000*1024^2)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
################################ Home Page ################################
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
callModule(module = homePage,
id = "HomePage")
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
################################ create the infercnv object ################################
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~ Gather the User Inputs ~~~~~~~~~~~~
## adding inputs (will be list like object)
infercnv_object_inputs <- callModule(module = createObjectInputs,
id = "create_object")
#~~~~~~~~~~~ run create the infercnv object ~~~~~~~~~~~
observeEvent(
# adding inputs (will be list like object)
input$create_obj,
{
tryCatch({
infercnv_obj_1 <<- callModule(module = createObject,
id = "create_object",
createObjectVars = infercnv_object_inputs)
},
error = function(e){
shinyalert::shinyalert(title = "Error!",
text = e$message,
type = "error")
})
}
)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
################################ Run Main Analysis ################################
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~ Gather the User Inputs ~~~~~~~~~~~~
## adding inputs (will be list like object)
infercnv_analysis_inputs <<- callModule(module = runInfercnvInputs,
id = "running_infercnv")
#~~~~~~~~~~~ Run Analysis ~~~~~~~~~~~~
observeEvent(
# run infercnv button
input$run_infercnv,
{
# run the infercnv analysis
if(!exists("infercnv_obj_1")){
print("no infercnv object")
insertUI(
# ID
selector = "#runAlertMessage",
# Make a class so can remove the message
ui = tags$div(
class = "alert alert-danger alert-dismissible",
shiny::HTML("<span class='fa fa-times fa-fw' aria-hidden='true'> </span> \
Upload Data Before Running Analysis \
<button type='button' \
class='close' data-dismiss='alert'>×</button>"))
)
}else{
# catch any errors that are output by the following modules
tryCatch({
# Run the analysis
infercnv_obj_2 <<- callModule(module = runInfercnv,
id = "running_infercnv",
infercnv_obj = infercnv_obj_1,
infercnv_inputs = infercnv_analysis_inputs)
# Module to run the analysis
callModule(module = mainAnalysis,
id = "output_main_analysis",
infercnv_inputs = infercnv_analysis_inputs,
infercnv_obj = infercnv_obj_2)
# Module to display the HMM analysis
callModule(module = hmmAnalysis,
id = "output_hmm_analysis",
infercnv_inputs = infercnv_analysis_inputs)
# Module to display the bayesian analysis
callModule(module = bayesianAnalysis,
id = "output_bayesian_analysis",
infercnv_inputs = infercnv_analysis_inputs)
# Moduel to create the diagnostic plots
callModule(module = diagnosticPlots,
id = "diagploting",
infercnv_inputs = infercnv_analysis_inputs)
# Median Filter post processing option
callModule(module = medianFilter,
id = "median_filter_output",
infercnv_inputs = infercnv_analysis_inputs,
infercnv_obj = infercnv_obj_2)
# Dynamic Bayesian and HMM plotting
callModule(module = adjustByProbThreshold,
id = "output_dynamic_analysis",
infercnv_inputs = infercnv_analysis_inputs)
# CNV and Cell probabilities
callModule(module = cnvCellProbs,
id = "cnv_cell_probs",
infercnv_inputs = infercnv_analysis_inputs)
# Message to user if succesful
insertUI(
# ID
selector = "#runAlertMessage",
# Make a class so can remove the message
ui = tags$div(
class = "alert alert-success alert-dismissible",
shiny::HTML("<span class='fa fa-check fa-fw' aria-hidden='true'> \
</span> Ran Analysis! <button type='button' \
class='close' data-dismiss='alert'>×</button>"))
)
},
error = function(e){
# print
shinyalert::shinyalert(title = "Error!",
text = e$message,
type = "error",
imageUrl = "https://cdn.pixabay.com/photo/2017/02/12/21/29/false-2061131_960_720.png")
})
}
}
)
# Option to Clear the output folder
observeEvent(
# run infercnv button
input$clear_output,
{
# check to see if infercnv was ran
if(!exists("infercnv_obj_2")){
insertUI(
# ID
selector = "#runAlertMessage",
# Make a class so can remove the message
ui = tags$div(
class = "alert alert-danger alert-dismissible",
shiny::HTML("<span class='fa fa-times fa-fw' aria-hidden='true'> </span> \
No Analysis was ran \
<button type='button' \
class='close' data-dismiss='alert'>×</button>"))
)
}else{
output_path <- infercnv_analysis_inputs$dir()
print(output_path)
print(file.exists(output_path))
unlink(x = output_path, recursive = TRUE)
futile.logger::flog.appender(futile.logger::appender.console())
insertUI(
# ID
selector = "#runAlertMessage",
# Make a class so can remove the message
ui = tags$div(
class = "alert alert-success alert-dismissible",
shiny::HTML("<span class='fa fa-check fa-fw' aria-hidden='true'> \
</span> Cleared Output Folder <button type='button' \
class='close' data-dismiss='alert'>×</button>"))
)
}
}
)
}
######################## Create App #########################
shinyApp(ui=ui, server = server)
broadinstitute/infercnvApp documentation built on Sept. 21, 2021, 4:17 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#!/usr/bin/env Rscript
################### Load the libraries and source modules ##########################
# Load libraries
library(shiny)
# source needed modules
source("createObject.R")
source("homePage.R")
source("runInfercnv.R")
source("mainAnalysisOutputTab.R")
source("bayesianAnalysisTab.R")
source("hmmAnalysisOutputTab.R")
source("adjustByProbThreshold.R")
source("diagnosticPlotTab.R")
source("medianFilterTab.R")
source("cnvCellProbsTab.R")
options(error = function() traceback(2))
options(shiny.reactlog=TRUE)
futile.logger::flog.appender(futile.logger::appender.console())
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Preform when the app is closed
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Remove the PDF files from the www folder when the app is closed
onStop(function(){
pdf_files <- list.files(path = "www",
pattern = "*.pdf",
all.files = FALSE,
full.names = TRUE)
unlink(pdf_files)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
######################## Set up the User Interface (UI) #########################
#' This is the user-interface definition of a Shiny web application
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ui <- tags$div(
class = "navbarMain",
shinyalert::useShinyalert(),
navbarPage(title = paste0("Infercnv-",packageVersion("infercnv")),
#----------- Set up the header and themes --------------
collapsible = FALSE,
inverse = TRUE,
windowTitle = "Infercnv",
position = "fixed-top",
############################# Home Tab #############################
tabPanel(title = shiny::HTML('<i class="fa fa-home fa-fw" aria-hidden="true"></i> Home'),
homePageUI("HomePage"),
),
############################# Upload and settings TAB ########################################
tabPanel(title = shiny::HTML('<i class="fa fa-file-text-o" aria-hidden="true"></i> Upload Files And Settings'),
#-------------------------- Create the infercnv Object --------------------------
createObjectInputsUI("create_object"),
# Add the action button
actionButton(inputId = "create_obj",
label = "Upload Data Files",
icon = icon(name = "cloud-upload-alt", lib = "font-awesome"),
width = '100%',
style="color: #fff; background-color: #68D77B"),
#-------------------------- Run Analysis --------------------------
tags$br(),
tags$hr(style="border-color: black;"),
tags$br(),
titlePanel(
tags$h1("Step 2: Settings And Run Analysis",
align = "center",
style = "background-color: #afc9eb;
color: black;
margin: -20px;
padding: 50px")
),
tags$br(),tags$br(),
# Run the module for infercnv analysis
runInfercnvUI("running_infercnv"),
# Create the button for running the infercnv analysis
actionButton(inputId = "run_infercnv",
label = " Run Infercnv",
icon = icon("refresh", lib = "font-awesome"),
width = '100%',
style="color: #fff; background-color: #68D77B"),
tags$br(),tags$br(),tags$br(),
# Button to clear the output folder
actionButton(inputId = "clear_output",
label = "Clear Output",
icon = icon("refresh", lib = "font-awesome"),
width = '100%',
style="color: #fff; background-color: red"),
tags$br(),tags$br(),tags$br(),
),
############################# Analysis Output tab #############################
tabPanel(title = shiny::HTML('<i class="fa fa-bar-chart" aria-hidden="true"></i> Analysis Output'),
tags$head(includeCSS("www/infercnv.style.css")),
tags$div(class = "navbarPageHome",
navbarPage(
title = "",
#-------------------------- Main Analysis Tab --------------------------
navbarMenu(
title = "Main Analysis Output",
tabPanel(title = "Main Analysis Output",
mainAnalysisTabUI("output_main_analysis")
),
tabPanel(title = "Median Filter Output",
medianFilterUI("median_filter_output")
)
),
#-------------------------- HMM Analysis Tab --------------------------
tabPanel(title = "HMM Analysis Output",
hmmAnalysisUI("output_hmm_analysis")
),
#-------------------------- Bayesian Analysis Tab --------------------------
navbarMenu(
title = "Bayesian Analysis Output",
tabPanel(title = "Bayesian Analysis Plots",
bayesianAnalysisUI("output_bayesian_analysis")
),
tabPanel(title = "Probability Plots",
cnvCellProbsUI("cnv_cell_probs")
)
),
#-------------------------- Dytnamic Analysis Tab --------------------------
tabPanel(title = "Dynamic Plots",
adjustByProbThresholdUI("output_dynamic_analysis")
),
#-------------------------- Supplemental Tab --------------------------
navbarMenu(
title = "Supplemental",
tabPanel(title = "Diagnostic Plots",
diagnosticPlotsUI("diagploting")
)
)
)
)
),
#Add a icon to the right of the navbar
tags$script(shiny::HTML("var header = $('.navbarMain > .navbar > .container-fluid');
header.append('<div style=\"float:right\"><i class=\"fa fa-dna fa-fw\" aria-hidden=\"true\" style=\"float:right; width:33px;height:41px;padding-top:20px;color:white\"></i> `</div>');
console.log(header)")
)
)
)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
######################## Set up the Server #########################
# This is the server logic of a Shiny web application. You can run the
# application by clicking 'Run App' above.
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
server <- function(input,
output,session){
# set the max upload size 1GB
options(shiny.maxRequestSize=10000*1024^2)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
################################ Home Page ################################
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
callModule(module = homePage,
id = "HomePage")
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
################################ create the infercnv object ################################
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~ Gather the User Inputs ~~~~~~~~~~~~
## adding inputs (will be list like object)
infercnv_object_inputs <- callModule(module = createObjectInputs,
id = "create_object")
#~~~~~~~~~~~ run create the infercnv object ~~~~~~~~~~~
observeEvent(
# adding inputs (will be list like object)
input$create_obj,
{
tryCatch({
infercnv_obj_1 <<- callModule(module = createObject,
id = "create_object",
createObjectVars = infercnv_object_inputs)
},
error = function(e){
shinyalert::shinyalert(title = "Error!",
text = e$message,
type = "error")
})
}
)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
################################ Run Main Analysis ################################
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~ Gather the User Inputs ~~~~~~~~~~~~
## adding inputs (will be list like object)
infercnv_analysis_inputs <<- callModule(module = runInfercnvInputs,
id = "running_infercnv")
#~~~~~~~~~~~ Run Analysis ~~~~~~~~~~~~
observeEvent(
# run infercnv button
input$run_infercnv,
{
# run the infercnv analysis
if(!exists("infercnv_obj_1")){
print("no infercnv object")
insertUI(
# ID
selector = "#runAlertMessage",
# Make a class so can remove the message
ui = tags$div(
class = "alert alert-danger alert-dismissible",
shiny::HTML("<span class='fa fa-times fa-fw' aria-hidden='true'> </span> \
Upload Data Before Running Analysis \
<button type='button' \
class='close' data-dismiss='alert'>×</button>"))
)
}else{
# catch any errors that are output by the following modules
tryCatch({
# Run the analysis
infercnv_obj_2 <<- callModule(module = runInfercnv,
id = "running_infercnv",
infercnv_obj = infercnv_obj_1,
infercnv_inputs = infercnv_analysis_inputs)
# Module to run the analysis
callModule(module = mainAnalysis,
id = "output_main_analysis",
infercnv_inputs = infercnv_analysis_inputs,
infercnv_obj = infercnv_obj_2)
# Module to display the HMM analysis
callModule(module = hmmAnalysis,
id = "output_hmm_analysis",
infercnv_inputs = infercnv_analysis_inputs)
# Module to display the bayesian analysis
callModule(module = bayesianAnalysis,
id = "output_bayesian_analysis",
infercnv_inputs = infercnv_analysis_inputs)
# Moduel to create the diagnostic plots
callModule(module = diagnosticPlots,
id = "diagploting",
infercnv_inputs = infercnv_analysis_inputs)
# Median Filter post processing option
callModule(module = medianFilter,
id = "median_filter_output",
infercnv_inputs = infercnv_analysis_inputs,
infercnv_obj = infercnv_obj_2)
# Dynamic Bayesian and HMM plotting
callModule(module = adjustByProbThreshold,
id = "output_dynamic_analysis",
infercnv_inputs = infercnv_analysis_inputs)
# CNV and Cell probabilities
callModule(module = cnvCellProbs,
id = "cnv_cell_probs",
infercnv_inputs = infercnv_analysis_inputs)
# Message to user if succesful
insertUI(
# ID
selector = "#runAlertMessage",
# Make a class so can remove the message
ui = tags$div(
class = "alert alert-success alert-dismissible",
shiny::HTML("<span class='fa fa-check fa-fw' aria-hidden='true'> \
</span> Ran Analysis! <button type='button' \
class='close' data-dismiss='alert'>×</button>"))
)
},
error = function(e){
# print
shinyalert::shinyalert(title = "Error!",
text = e$message,
type = "error",
imageUrl = "https://cdn.pixabay.com/photo/2017/02/12/21/29/false-2061131_960_720.png")
})
}
}
)
# Option to Clear the output folder
observeEvent(
# run infercnv button
input$clear_output,
{
# check to see if infercnv was ran
if(!exists("infercnv_obj_2")){
insertUI(
# ID
selector = "#runAlertMessage",
# Make a class so can remove the message
ui = tags$div(
class = "alert alert-danger alert-dismissible",
shiny::HTML("<span class='fa fa-times fa-fw' aria-hidden='true'> </span> \
No Analysis was ran \
<button type='button' \
class='close' data-dismiss='alert'>×</button>"))
)
}else{
output_path <- infercnv_analysis_inputs$dir()
print(output_path)
print(file.exists(output_path))
unlink(x = output_path, recursive = TRUE)
futile.logger::flog.appender(futile.logger::appender.console())
insertUI(
# ID
selector = "#runAlertMessage",
# Make a class so can remove the message
ui = tags$div(
class = "alert alert-success alert-dismissible",
shiny::HTML("<span class='fa fa-check fa-fw' aria-hidden='true'> \
</span> Cleared Output Folder <button type='button' \
class='close' data-dismiss='alert'>×</button>"))
)
}
}
)
}
######################## Create App #########################
shinyApp(ui=ui, server = server)
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.