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############################################################################
# USER INTERFACE (UI) DEFINITION
############################################################################
# Define the web application's user interface using Shiny's fluidPage layout
# The UI consists of a header, mode selection, sidebar controls, and main plot panel
# Core Shiny framework for building interactive web applications
library(shiny)
# Visualization and UI enhancement packages
library(shinyBS) # Bootstrap components for Shiny (tooltips, modals, etc.)
ui <- fluidPage(
#--------------------------------------------------------------------------
# APPLICATION HEADER
#--------------------------------------------------------------------------
# Create header row with application title and help button
fluidRow(
# Application title in a responsive column
column(3, titlePanel("VisioProt-MS")),
# Help button that opens documentation in a new browser tab
column(1, actionButton(inputId='ab1', label="",
icon = icon("fa-solid fa-circle-question"),
onclick ="window.open('https://masstools.ipbs.fr/visioprothelp.html', '_blank')",
style="color: #fff; background-color: #673a49; border-color: #000000"),
bsTooltip("ab1",
"go to help page",
placement = "bottom")
)
),
# Custom CSS styling for the help button
tags$style(type='text/css', "#ab1 { width:80%; margin-top: 25px; font-family : Cursive; font-weight: 900; font-size: 160%;}"),
#--------------------------------------------------------------------------
# MODE SELECTION
#--------------------------------------------------------------------------
# Allow users to choose between MS-only visualization or MS/MS overlay mode
#checkboxInput("MSModeCheck", "MS data only", TRUE), # Legacy checkbox implementation
# Radio buttons for mode selection (replaces checkbox for better UX)
radioButtons("MSModeCheck", "MS mode:",
c("MS" = 'MS', # MS data visualization only
"MS/MS" = 'MS2'), # MS data with MS/MS identification overlay
selected = 'MS', # Default to MS mode
inline = TRUE # Display options horizontally
),
# Tooltip explaining the mode selection options
bsTooltip("MSModeCheck",
"Choose between plotting MS data only or overlaying results of Top-Down searches",
"right"),
#--------------------------------------------------------------------------
# MAIN LAYOUT: SIDEBAR AND PLOT PANEL
#--------------------------------------------------------------------------
# Create two-panel layout with sidebar controls and main plotting area
sidebarLayout(
#------------------------------------------------------------------------
# SIDEBAR PANEL: USER CONTROLS AND FILE INPUTS
#------------------------------------------------------------------------
sidebarPanel(width = 4,
#====================================================================
# CONDITIONAL PANELS: DIFFERENT CONTROLS FOR EACH MODE
#====================================================================
#--------------------------------------------------------------------
# MS MODE PANEL: For MS data visualization only
#--------------------------------------------------------------------
conditionalPanel(condition="input.MSModeCheck== 'MS'",
#--------------------------------------------------------
# File Input Section for MS Mode
#--------------------------------------------------------
# Allow users to upload deconvoluted MS data files
fileInput("fileMS", "Select input file(s):",
accept = c(
"text/csv", # CSV files
"text/comma-separated-values,text/plain", # Text files
".txt", # Text files
".ms1ft", # ProMex format
".csv", # CSV files
".msalign"), # TopPIC format
multiple = T, # Allow multiple files for comparison
width = "100%"
),
#--------------------------------------------------------
# Test Mode Controls for MS Mode
#--------------------------------------------------------
# Enable test mode to try the application with sample data
checkboxInput("TestModeCheck", "Using test mode", FALSE),
bsTooltip("TestModeCheck",
"Check to test the application without uploading any file. Then click on a button to upload a single test file or several for overlay",
"right"),
# Show test file buttons only when test mode is enabled
conditionalPanel(condition="input.TestModeCheck==true",
actionButton("TestFile1", "Single test file"), # Load one sample file
actionButton("TestFile2", "Multiple test files") # Load multiple files for comparison
)
),
#--------------------------------------------------------------------
# MS/MS MODE PANEL: For MS data with identification overlay
#--------------------------------------------------------------------
conditionalPanel(condition="input.MSModeCheck== 'MS2'",
#--------------------------------------------------------
# Test Mode Controls for MS/MS Mode
#--------------------------------------------------------
checkboxInput("MS2TestModeCheck", "Using test mode", FALSE),
bsTooltip("MS2TestModeCheck",
"Check to test the application without uploading any file",
"right"),
# Display warning message when in test mode
conditionalPanel(condition = "input.MS2TestModeCheck==true",
tags$span(style="color:red", "You are in test mode. Click on a button to select a single test file or multiple test files.\nUncheck to exit and upload your own data."),
br()
),
#--------------------------------------------------------
# File Input Section for MS/MS Mode (User Data)
#--------------------------------------------------------
conditionalPanel(condition = "input.MS2TestModeCheck==false",
# MS data file input (background for MS/MS overlay)
fileInput("fileMS2", "Select input file for MS:",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv",
".txt",
".ms1ft", # ProMex format
".msalign"), # TopPIC format
multiple = F, # Single file only for background MS
width = "100%"
),
#------------------------------------------------
# Software Selection for MS/MS Analysis
#------------------------------------------------
# Choose which top-down software was used for analysis
radioButtons("PDPFModeCheck", "Origin of the MS/MS files:",
c("Proteome Discoverer" = 'PD', # Thermo Fisher
"MSPathFinder" = 'PF', # PNNL
"TopPIC" = 'TP'), # UCSD
selected = 'PD',
inline = TRUE
),
bsTooltip("PDPFModeCheck",
"Choose the software utilized for analysing of the top-down data",
"right"),
#============================================
# PROTEOME DISCOVERER FILE INPUTS
#============================================
# Proteome Discoverer requires two files:
# 1. MSMSSpectrumInfo: MS/MS spectrum metadata
# 2. PSM: Peptide spectrum matches with protein IDs
conditionalPanel(condition = "input.PDPFModeCheck== 'PD'",
fileInput("MS2file", "Choose MSMSSpectrumInfo File:",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".txt")
),
fileInput("PSMfile", "Choose PSM File:",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".txt")
)),
#============================================
# MSPATHFINDER FILE INPUTS
#============================================
# MSPathFinder requires IcTarget or IcTda results file
conditionalPanel(condition = "input.PDPFModeCheck== 'PF'",
fileInput("MS2filePF", "Choose IcTarget or IcTda File from MSPathFinder:",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".tsv") # Tab-separated values
)
),
#============================================
# TOPPIC FILE INPUTS
#============================================
# TopPIC requires two files:
# 1. MS/MS data file (.msalign format)
# 2. Identification results (OUTPUT_TABLE)
conditionalPanel(condition = "input.PDPFModeCheck== 'TP'",
fileInput("MS2fileTP", "Choose MS/MS File:",
accept = c(
"text",
"text/comma-separated-values,text/plain",
".msalign") # TopPIC MS/MS format
),
fileInput("IDfileTP", "Choose the OUTPUT_TABLE/_ms2_toppic (saved at tab-delimited .txt) from TopPIC:",
accept = c(
"text",
"text/comma-separated-values,text/plain",
".OUTPUT_TABLE") # TopPIC results format
)
)
),
#--------------------------------------------------------
# Protein Selection and Display Options for MS/MS Mode
#--------------------------------------------------------
# Dropdown to select which identified proteins to highlight in the plot
selectInput("SelectProt", "Select the ID to highlight:",
NULL, # Options will be populated dynamically based on loaded data
multiple = TRUE), # Allow multiple protein selection
bsTooltip("SelectProt",
"Select among the identified proteins which one(s) to highlight on the plot",
"right"),
# Option to hide MS/MS spectra without protein identification
checkboxInput("HideMSMS", "Hide MS/MS withouth ID", FALSE),
bsTooltip("HideMSMS",
"Removes the MS/MS spectra from the top-down analysis that were not matched to a protein.",
"right"),
# Option to show/hide the underlying MS1 trace
checkboxInput("MSTrace", "Display the MS trace", TRUE),
bsTooltip("MSTrace",
"Adds the MS trace to the plot.",
"right")
),
#====================================================================
# COMMON CONTROLS: Available in both MS and MS/MS modes
#====================================================================
# Toggle between static ggplot2 and interactive plotly visualization
checkboxInput("DataPoints", "Show data labels (slower)", FALSE),
bsTooltip("DataPoints",
"Switch to \"data\" mode: data appears on hovering",
"right"),
#--------------------------------------------------------------------
# PLOT CUSTOMIZATION PARAMETERS
#--------------------------------------------------------------------
# Arrange plot parameters in a responsive row layout
fluidRow(
#------------------------------------------------------------------
# Color Scale Selection (Column 1)
#------------------------------------------------------------------
column(5,
# Color palette selection - options change based on number of files loaded
selectInput("colourscale", "Colour scale:",
c("Spectral" = "Spectral", # For single files: continuous scales
"Red/yellow/blue" = "RdYlBu",
"Red/yellow/green" = "RdYlGn",
"yellow to red" = "YlOrRd"
)),
bsTooltip("colourscale",
"Select the colour scale for the MS data.",
"right")),
#------------------------------------------------------------------
# Point Size Control (Column 2)
#------------------------------------------------------------------
column(3,
numericInput("pch", label = "Point size:", value = 1, min = 0.1, step = 0.1, max = 10),
bsTooltip("pch",
"Define the size of the point (from 0.1 to 10).",
"right")),
#------------------------------------------------------------------
# Intensity Threshold Control (Column 3)
#------------------------------------------------------------------
column(4,
numericInput("IntensityThresh", label = "Threshold:", value = 20, min = 0, max = 100, step = 1),
bsTooltip("IntensityThresh",
"Define the percentage of highest intensity features of the MS data to display.",
"right"))
),
#--------------------------------------------------------
# Signal sum for MS Mode
#--------------------------------------------------------
# Click to calculate the sum of signal in plot window
# conditionalPanel(condition="input.MSModeCheck== 'MS' && output.filetype.RoWinPro == 0 && !(output.filetype.BioPharma == 0 && output.filetype.ProMex == 0)",
conditionalPanel(condition="input.MSModeCheck== 'MS' && output.show_calcsum",
actionButton("CalcSum", "Sum signal in plot",
style="color: #fff; background-color: #3c3c3c; border-color: #3c3c3c"),
bsTooltip("CalcSum",
"Clic to calculate sum of signal of plotted points",
"right"),
actionButton("CalcSumReset", "Reset",
style="color: #fff; background-color: #3c3c3c; border-color: #3c3c3c"),
bsTooltip("CalcSumReset",
"Clic to reset values",
"right"),
tableOutput('SumSignal')
),
#--------------------------------------------------------------------
# ZOOM AND NAVIGATION CONTROLS
#--------------------------------------------------------------------
# Dynamic instructions that change based on plot type (static vs interactive)
hr(),
htmlOutput("ZoomParam"),
br(),
# Zoom control buttons
actionButton("DeZoom", "Unzoom one step", style='padding:8px; font-size:100%'),
bsTooltip("DeZoom",
"Unzoom to previous window (only once).",
"right"),
actionButton("TotalDeZoom", "Total unzoom", style='padding:8px; font-size:100%'),
bsTooltip("TotalDeZoom",
"Total unzoom.",
"right"),
br(),
br(),
#--------------------------------------------------------------------
# EXPORT CONTROLS: Download plot in different formats
#--------------------------------------------------------------------
downloadButton("Download", "Download .pdf"), # PDF format for publications
downloadButton("Download1", "Download .png"), # PNG format for presentations
downloadButton("Download2", "Download .svg"), # SVG format for vector graphics
downloadButton("Download3", "Download table"), # tab-delimited file with values
#--------------------------------------------------------------------
# CITATION INFORMATION
#--------------------------------------------------------------------
HTML(paste("<br/><br/>",
h5("If you use VisioProt-MS for your research please cite:"),
"Marie Locard-Paulet, Julien Parra, Renaud Albigot, Emmanuelle Mouton-Barbosa, Laurent Bardi, Odile Burlet-Schiltz, Julien Marcoux; VisioProt-MS: interactive 2D maps from intact protein mass spectrometry, Bioinformatics, bty680, https://doi.org/10.1093/bioinformatics/bty680")
)
),
#--------------------------------------------------------------------------
# MAIN PANEL: Plot display area
#--------------------------------------------------------------------------
# Main plotting area that adapts based on user's visualization choice
# (static ggplot2 vs interactive plotly)
mainPanel(width = 8,
uiOutput("plotUI"), # Dynamic UI element for plot output
## if MS1 panel, plot the sum of intensities in the plot window
# if (print_sum_results) { #TODO: conditional: only if MS trace panel
uiOutput("sum_results") # Dynamic UI element for printing intensity summarization results
# }
)
),
#----------------------------------------------------------------------------
# FOOTER
#----------------------------------------------------------------------------
# Application footer with copyright information
tabsetPanel(
tabPanel(
HTML('<footer><font size="0.8">copyright 2017 - CNRS - All rights reserved - VisioProt-MS V2.4</font></footer>')
)
)
)