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ui.R
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ui.R
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# Define UI for data upload app ----
ui <- function(request){shinyUI(
dashboardPage(
skin = "blue",
dashboardHeader(title = "LFQ-Analyst"),
# disable = TRUE),# Disable title bar
dashboardSidebar(
useShinyalert(),
sidebarMenu(
id="tabs_selected",
convertMenuItem(menuItem('Home', icon=icon("home"), selected = TRUE, tabName = "home"), tabName = "home"),
convertMenuItem(menuItem("Analysis", tabName="analysis", icon=icon("flask"),
#menuItem("Input Files", tabName="file", icon=icon("file"), #selected = TRUE,
fileInput('file1',
'Upload MaxQuant ProteinGroups.txt',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv')),
fileInput('file2',
'Upload Experimental Design Matrix',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv')),
# ),
tags$hr(),
menuItem("Advanced Options",tabName="advanced", icon = icon("cogs"),
numericInput("p",
"Adjusted p-value cutoff",
min = 0.0001, max = 0.1, value = 0.05),
numericInput("lfc",
"Log2 fold change cutoff",
min = 0, max = 10, value = 1),
checkboxInput("paired",
"Paired test", FALSE),
radioButtons("imputation",
"Imputation type",
choices = c("Perseus-type"="man", MSnbase::imputeMethods())[1:9],
selected = "man"),
radioButtons("fdr_correction",
"Type of FDR correction",
choices = c("Benjamini Hochberg"="BH",
"t-statistics-based"="fdrtool"
), selected= "BH"),
checkboxInput("single_peptide",
"Include single peptide identifications", FALSE),
numericInput("k_number",
"Number of clusters in heatmap",
min = 1, max = 20, value = 6)
),
tags$hr(),
actionButton("analyze", "Start Analysis"),
tags$hr(),
p(a("Example LFQ data", target= "_blank",
href="data/proteinGroups_example.txt",
download="proteinGroups_example.txt")),
p(a("Example Experimental Design file", target= "_blank",
href="data/experimental_design_example.txt",
download="experimental_design_example.txt"))
#,
#actionButton("load_data", "Load example data")
), tabName = 'analysis'),
convertMenuItem(menuItem('Demo', icon=icon("eye"), tabName = "demo"), tabName = "demo"),
convertMenuItem(menuItem('User Guide', icon=icon("question"),
#href = "https://monashbioinformaticsplatform.github.io/LFQ-Analyst/",
tabName = "info"), tabName = "info")
)
), # sidebar close
################################################################
## DASHBOARD BODY
################################################################
dashboardBody(
useShinyjs(), #imp to use shinyjs functions
tags$head(includeScript("google_analytics.js")),
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "./css/custom.css")
),
# Add logo to the body
# tags$img(src="mbpf_logo.jpg",height=50, align="right"),
## Add tabItems
# id="body",
tabItems(
tabItem(tabName = "home",
fluidRow(
box(
title = "Overview",
h3("LFQ-Analyst: An easy-to-use interactive web-platform to analyze and visualize proteomics data
preprocessed with MaxQuant."),
p("LFQ-Analyst is an easy-to-use, interactive web application developed to perform
differential expression analysis with “one click” and to visualize label-free quantitative proteomic
datasets preprocessed with MaxQuant. LFQ-Analyst provides a wealth of user-analytic features
and offers numerous publication-quality result output graphics and tables to facilitate statistical
and exploratory analysis of label-free quantitative datasets. "),
br(),
HTML('<center><img src="./LFQ_analyst.svg" width="600px"></center>'),
br(),
h4("Sidebar tabs"),
tags$ul(
tags$li(tags$b("Analysis: "),"perform your own analysis"),
tags$li(tags$b("Demo: "),"familiarise yourself with LFQ-Analyst by browsing through pre-analysed results"),
tags$li(tags$b("User Guide: "), "download an in-depth manual")
),
width = 12,
solidHeader = TRUE,
status = "primary"
)#box 1 closed
) #fluidrow close
), # home tab close
tabItem(tabName = "analysis",
div(id="quickstart_info",
fluidPage(
box(
title = "Getting Started",
h3(tags$b(span("Quick Start", style="text-decoration:underline"))),
tags$ul(
tags$li("Upload your ", tags$b("proteinGroups.txt "), "generated by MaxQuant."),
tags$li("Upload your ", tags$b(" experimental design "),"table. "),
tags$li(tags$b("Optional: "),"Adjust the p-value cut-off, the log2 fold change cut-off,
the imputation type, FDR correction method and/or number of clusters in heatmap
in the", tags$b("Advanced Options")),
tags$li("Press ", tags$b("'Start Analysis' ")),
tags$li(tags$b("Hint: "), " Use the ", tags$b("User Guide ")," tab for a detailed explanation of inputs,
advanced options and outputs"),
tags$li(tags$b("Note: "), " The experimental design file is not the" , tags$b("'mqpar.xml' "),"file
from MaxQuant. Use the example file template provided.")
),
br(),
HTML('<center><img src="./LFQ_analyst.svg" width="500px"></center>'),
width = 12,
solidHeader = TRUE,
status = "danger"
)
)
), # QUICKSTART INFO CLOSE
shinyjs::hidden(div(id="downloadbox",
fluidRow(
box(
column(6,uiOutput("downloadTable"),offset = 1),
column(4,uiOutput("downloadButton")), # make the button on same line
width = 4),
infoBoxOutput("significantBox",width = 4),
box(
column(5,uiOutput("downloadreport")), # offset for dist between buttons
#tags$br(),
#column(5,uiOutput('downloadPlots')),
width = 4
)
))), #close div and first row
# align save button
tags$style(type='text/css', "#downloadButton { width:100%; margin-top: 25px;}"),
tags$style(type='text/css', "#downloadreport { width:100%; vertical-align- middle; margin-top: 25px;
margin-bottom: 25px;}"),
#tags$style(type='text/css', "#downloadPlots { width:100%; margin-top: 25px;}"),
tags$br(), # Blank lines
tags$br(),
## Data table and result plots box
fluidRow(
shinyjs::hidden(div(id="results_tab",
box(
title = "LFQ Results Table",
DT::dataTableOutput("contents"),
# actionButton("clear", "Deselect Rows"),
actionButton("original", "Refresh Table"),
width = 6,
status = "success",
#color=""
solidHeader = TRUE
),
# column(
box(
width= 6,
collapsible = TRUE,
#status="primary",
#solidHeader=TRUE,
tabBox(
title = "Result Plots",
width = 12,
tabPanel(title = "Volcano plot",
fluidRow(
box(uiOutput("volcano_cntrst"), width = 5),
box(numericInput("fontsize",
"Font size",
min = 0, max = 8, value = 4),
width = 3),
box(checkboxInput("check_names",
"Display names",
value = FALSE),
checkboxInput("p_adj",
"Adjusted p values",
value = FALSE),
width = 4),
tags$p("Select protein from LFQ Results Table to highlight on the plot OR
drag the mouse on plot to show expression of proteins in Table")
#Add text line
# tags$p("OR"),
# tags$p("Drag the mouse on plot to show expression of proteins in Table")
),
fluidRow(
plotOutput("volcano", height = 600,
# hover = "protein_hover"),
#),
# click = "protein_click"),
brush = "protein_brush",
click = "protein_click"),
downloadButton('downloadVolcano', 'Save Highlighted Plot'),
actionButton("resetPlot", "Clear Selection")
#)),
)),
tabPanel(title= "Heatmap",
fluidRow(
plotOutput("heatmap", height = 600)
),
fluidRow(
box(numericInput("cluster_number",
"Cluster to download",
min=1, max=6, value = 1), width = 6),
box(downloadButton('downloadCluster',"Save Cluster"),
downloadButton('download_hm_svg', "Save svg"),
width = 5)
)
),
tabPanel(title = "Protein Plot",
fluidRow(
box(radioButtons("type",
"Plot type",
choices = c("Box Plot"= "boxplot",
"Violin Plot"="violin",
"Interaction Plot"= "interaction",
"Intensity Plot"="dot"
),
selected = "boxplot",
inline = TRUE),
width = 12
),
tags$p("Select one or more rows from LFQ Results Table to plot individual
protein intesities across conditions and replicates")
),
fluidRow(
plotOutput("protein_plot"),
downloadButton('downloadProtein', 'Download Plot')
)
)
# verbatimTextOutput("protein_info"))
)
) # box or column end
))),
## QC Box
fluidRow(
shinyjs::hidden(div(id="qc_tab",
column(
width=6,
tabBox(title = "QC Plots", width = 12,
tabPanel(title = "PCA Plot",
plotOutput("pca_plot", height=600),
downloadButton('download_pca_svg', "Save svg")
),
tabPanel(title="Sample Correlation",
plotOutput("sample_corr", height = 600),
downloadButton('download_corr_svg', "Save svg")
),
tabPanel(title= "Sample CVs",
plotOutput("sample_cvs", height = 600),
downloadButton('download_cvs_svg', "Save svg")
),
tabPanel(title = "Protein Numbers",
plotOutput("numbers", height = 600),
downloadButton('download_num_svg', "Save svg")
),
tabPanel(title = "Sample coverage",
plotOutput("coverage", height = 600),
downloadButton('download_cov_svg', "Save svg")
),
tabPanel(title = "Normalization",
plotOutput("norm", height = 600),
downloadButton('download_norm_svg', "Save svg")
),
# tabPanel(title = "Missing values - Quant",
# plotOutput("detect", height = 600)
# ),
tabPanel(title = "Missing values - Heatmap",
plotOutput("missval", height = 600),
downloadButton('download_missval_svg', "Save svg")
),
tabPanel(title = "Imputation",
plotOutput("imputation", height = 600),
downloadButton('download_imp_svg', "Save svg")
)#,
# tabPanel(title = "p-value Histogram",
# plotOutput("p_hist", height = 600)
# )
) # Tab box close
),
column(
width=6,
tabBox(title = "Enrichment", width = 12,
tabPanel(title="Gene Ontology",
box(uiOutput("contrast"), width = 5),
box(
selectInput("go_database", "GO database:",
c("Molecular Function"="GO_Molecular_Function_2017b",
"Cellular Component"="GO_Cellular_Component_2017b",
"Biological Process"="GO_Biological_Process_2017b")),
width= 5),
actionButton("go_analysis", "Run Enrichment"),
plotOutput("go_enrichment"),
downloadButton('downloadGO', 'Download Table')
),
tabPanel(title= "Pathway enrichment",
box(uiOutput("contrast_1"), width = 5),
box(
selectInput("pathway_database", "Pathway database:",
c("KEGG"="KEGG_2016",
"Reactome"="Reactome_2016")),
width= 5),
actionButton("pathway_analysis", "Run Enrichment"),
plotOutput("pathway_enrichment"),
downloadButton('downloadPA', 'Download Table')
)
) # Tab box close
)
))) # fluidrow qc close
#bookmarkButton()
), #analysis tab close
tabItem(tabName = "info",
fluidRow(
box(
title = "User Guide",
h3("LFQ-Analyst: Manual"),
# div(p(HTML(paste0('A detail online user manual can be accessed ',
# a(href = 'https://monashbioinformaticsplatform.github.io/LFQ-Analyst/',
# target='_blank', 'here'))))),
div(p(HTML(paste0("A detailed user manual can be accessed",
a(href = './LFQ-Analyst_manual.pdf',
target='_blank', tags$b("here.")))))),
h4("Contact Us"),
p("For any feedback or question regarding LFQ-Analyst, please contact the
Monash Proteomics and Metabolomics Facility:"),
tags$ul(
tags$li("Anup Shah: anup.shah(at)monash.edu"),
tags$li("Ralf Schittenhelm: ralf.schittenhelm(at)monash.edu")
),
h4("How to Cite LFQ-Analyst?"),
div(p(HTML(paste0("Please Cite: Shah AD, Goode RJA, Huang C, Powell DR, Schittenhelm RB.
LFQ-Analyst: An easy-to-use interactive web-platform to analyze and
visualize proteomics data preprocessed with MaxQuant. DOI:",
a(href = 'https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00496',
target='_blank', tags$b("10.1021/acs.jproteome.9b00496")))))),
h4("News and Updates"),
tags$ul(
tags$li("27-12-2021: LFQ-Analyst being accessed by more than 5000 users worldwide"),
tags$li("30-09-2021: LFQ-Analyst being accessed by more than 4000 users worldwide"),
tags$li("03-05-2021: LFQ-Analyst being accessed by more than 3000 users worldwide"),
tags$li("24-02-2021: Correlation plot now use all protein expression data"),
tags$li("25-11-2020: LFQ-Analyst being accessed by more than 2000 users worldwide"),
tags$li("07-04-2020: LFQ-Analyst being accessed by more than 1000 users worldwide"),
tags$li("03-01-2020: LFQ-Analyst manuscript published in volume 19 of JPR"),
tags$li("28-10-2019: LFQ-Analyst paper published online in Journal of Proteome Research (JPR)"),
tags$li("02-10-2019: Svg figures download feature added"),
tags$li("09-09-2019: Paired test support added"),
tags$li("09-09-2019: Option to include single peptide observations in the analysis"),
tags$li("19-02-2019: LFQ-Analyst made public")
),
width = 12,
solidHeader = TRUE,
status = "primary"
) #includeMarkdown("www/Info.md")
)
),# info tab close
tabItem(tabName = "demo",
div(id="downloadbox_dm",
fluidRow(
box(
column(6,uiOutput("downloadTable_dm"),offset = 1),
column(4,uiOutput("downloadButton_dm")), # make the button on same line
width = 4),
infoBoxOutput("significantBox_dm",width = 4),
box(
column(5,uiOutput("downloadreport_dm")), # offset for dist between buttons
#tags$br(),
# column(5,uiOutput('downloadPlots_dm')),
width = 4
)
)), #close div and first row
# align save button
tags$style(type='text/css', "#downloadButton_dm { width:100%; margin-top: 25px;}"),
tags$style(type='text/css', "#downloadreport_dm { width:100%; margin-top: 25px; margin-bottom: 25px;}"),
# tags$style(type='text/css', "#downloadPlots_dm { width:100%; margin-top: 25px;}"),
tags$br(), # Blank lines
tags$br(),
## Data table and result plots box
fluidRow(
div(id="results_tab_dm",
box(
title = "LFQ Results Table",
DT::dataTableOutput("contents_dm"),
# actionButton("clear", "Deselect Rows"),
actionButton("original_dm", "Refresh Table"),
width = 6,
status = "success",
#color=""
solidHeader = TRUE
),
# column(
box(
width= 6,
collapsible = TRUE,
#status="primary",
#solidHeader=TRUE,
tabBox(
title = "Result Plots",
width = 12,
tabPanel(title = "Volcano plot",
fluidRow(
box(uiOutput("volcano_cntrst_dm"), width = 5),
box(numericInput("fontsize_dm",
"Font size",
min = 0, max = 8, value = 4),
width = 3),
box(checkboxInput("check_names_dm",
"Display names",
value = FALSE),
checkboxInput("p_adj_dm",
"Adjusted p values",
value = FALSE),
width = 4),
tags$p("Select protein from LFQ Results Table to highlight on the plot OR
drag the mouse on plot to show expression of proteins in Table")
#Add text line
# tags$p("OR"),
# tags$p("Drag the mouse on plot to show expression of proteins in Table")
),
fluidRow(
plotOutput("volcano_dm", height = 600,
# hover = "protein_hover"),
#),
# click = "protein_click"),
brush = "protein_brush_dm",
click = "protein_click_dm"),
downloadButton('downloadVolcano_dm', 'Save Highlighted Plot'),
actionButton("resetPlot_dm", "Clear Selection")
#)),
)),
tabPanel(title= "Heatmap",
fluidRow(
plotOutput("heatmap_dm", height = 600)
),
fluidRow(
box(numericInput("cluster_number_dm",
"Cluster to download",
min=1, max=6, value = 1), width = 6),
box(downloadButton('downloadCluster_dm',"Save Cluster"),width = 3)
)
),
tabPanel(title = "Protein Plot",
fluidRow(
box(radioButtons("type_dm",
"Plot type",
choices = c("Box Plot"= "boxplot",
"Violin Plot"="violin",
"Interaction Plot"= "interaction",
"Intensity Plot"="dot"
),
selected = "boxplot",
inline = TRUE),
width = 12
),
tags$p("Select one or more rows from LFQ Results Table to plot individual
protein intesities across conditions and replicates")
),
fluidRow(
plotOutput("protein_plot_dm"),
downloadButton('downloadProtein_dm', 'Download Plot')
)
)
# verbatimTextOutput("protein_info"))
)
) # box or column end
)),
## QC Box
fluidRow(
div(id="qc_tab_dm",
column(
width=6,
tabBox(title = "QC Plots", width = 12,
tabPanel(title = "PCA Plot",
plotOutput("pca_plot_dm"), height=600),
tabPanel(title="Sample Correlation",
plotOutput("sample_corr_dm", height = 600)
),
tabPanel(title= "Sample CVs",
plotOutput("sample_cvs_dm", height = 600)
),
tabPanel(title = "Protein Numbers",
plotOutput("numbers_dm", height = 600)
),
tabPanel(title = "Sample coverage",
plotOutput("coverage_dm", height = 600)
),
tabPanel(title = "Normalization",
plotOutput("norm_dm", height = 600)
),
# tabPanel(title = "Missing values - Quant",
# plotOutput("detect_dm", height = 600)
# ),
tabPanel(title = "Missing values - Heatmap",
plotOutput("missval_dm", height = 600)
),
tabPanel(title = "Imputation",
plotOutput("imputation_dm", height = 600)
)#,
# tabPanel(title = "p-value Histogram",
# plotOutput("p_hist_dm", height = 600)
# )
) # Tab box close
),
column(
width=6,
tabBox(title = "Enrichment", width = 12,
tabPanel(title="Gene Ontology",
box(uiOutput("contrast_dm"), width = 5),
box(
selectInput("go_database_dm", "GO database:",
c("Molecular Function"="GO_Molecular_Function_2017b",
"Cellular Component"="GO_Cellular_Component_2017b",
"Biological Process"="GO_Biological_Process_2017b")),
width= 5),
actionButton("go_analysis_dm", "Run Enrichment"),
plotOutput("go_enrichment_dm"),
downloadButton('downloadGO_dm', 'Download Table')
),
tabPanel(title= "Pathway enrichment",
box(uiOutput("contrast_dm_1"), width = 5),
box(
selectInput("pathway_database_dm", "Pathway database:",
c("KEGG"="KEGG_2016",
"Reactome"="Reactome_2016")),
width= 5),
actionButton("pathway_analysis_dm", "Run Enrichment"),
plotOutput("pathway_enrichment_dm"),
downloadButton('downloadPA_dm', 'Download Table')
) #### Tab demo closed
) # Tab box close
)
)) # fluidrow qc close
# tabItems(
) # Tab items close
#)# info tab lose
# )#tabitems close
),
tags$footer(
tags$p("Supported by: Monash Proteomics and Metabolomics Facility & Monash Bioinformatics Platform,
Monash University"),
align = "right") # Dasbboardbody close
) #Dashboard page close
)
)#Shiny U Close
}