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ui.R
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ui.R
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# Define UI for data upload app ----
VERSION <- "v0.39"
DEBUG <- F
ENABLE_PEPTIDE_ANALYSIS <- T
if (ENABLE_PEPTIDE_ANALYSIS) {
analysis_options <- c("LFQ"="LFQ", "TMT"="TMT", "DIA"="DIA",
"LFQ (peptide)"="LFQ-peptide", "TMT (peptide)"="TMT-peptide", "DIA (peptide)"= "DIA-peptide")
} else {
analysis_options <- c("LFQ"="LFQ", "TMT"="TMT", "DIA"="DIA")
}
ui <- function(request){shinyUI(
dashboardPage(
skin = "black",
dashboardHeader(title = "BCM LysoProteomics-Analyst"),
# disable = TRUE),# Disable title bar
dashboardSidebar(
sidebarMenu(
id="tabs_selected",
convertMenuItem(
tabName = "home",
menuItem('Home', icon=icon("home"), selected = TRUE, tabName = "home")
),
convertMenuItem(
tabName = 'analysis',
menuItem("Analysis", tabName="analysis", icon=icon("flask"),
selectInput("exp", "Data type:", analysis_options, selected = "LFQ"),
conditionalPanel(
condition = "input.exp == 'LFQ'",
fileInput('lfq_expr', 'Upload FragPipe combined_protein.tsv',
accept=c('text/tsv',
'text/tab-separated-values,text/plain',
'.tsv')),
fileInput('lfq_manifest', 'Upload experimental design template/annotation',
accept=c('text/tsv',
'text/tab-separated-values,text/plain',
'.tsv')),
radioButtons("lfq_type",
"Intensity Type",
choices = c("Intensity"="Intensity",
"MaxLFQ Intensity"="MaxLFQ",
"Spectral Count"="Spectral Count"),
selected = "Intensity"),
tags$hr(),
downloadLink("lfq_example", label="Example LFQ data"),
br(),
downloadLink("lfq_annotation", label="Example annotation")),
conditionalPanel(
condition = "input.exp == 'TMT'",
fileInput('tmt_expr', 'Upload gene-level or protein-level TMT-I report *.tsv',
accept=c('text/tsv',
'text/tab-separated-values,text/plain',
'.tsv')),
fileInput('tmt_annot', 'Upload experimental design template/annotation',
accept=c('text/tsv',
'text/tab-separated-values,text/plain',
'.tsv'))
),
conditionalPanel(
condition = "input.exp == 'DIA'",
fileInput('dia_expr', 'Upload protein group (PG) matrix *.tsv',
accept=c('text/tsv',
'text/tab-separated-values,text/plain',
'.tsv')),
fileInput('dia_manifest', 'Upload experimental design template/annotation',
accept=c('text/tsv',
'text/tab-separated-values,text/plain',
'.tsv'))),
conditionalPanel(
condition = "input.exp == 'LFQ-peptide'",
fileInput('lfq_pept_expr', 'Upload combined_peptide.tsv',
accept=c('text/tsv',
'text/tab-separated-values,text/plain',
'.tsv')),
fileInput('lfq_pept_annot', 'Upload experimental design template/annotation',
accept=c('text/tsv',
'text/tab-separated-values,text/plain',
'.tsv')),
radioButtons("lfq_pept_type",
"Intensity Type",
choices = c("Intensity"="Intensity",
"MaxLFQ Intensity"="MaxLFQ",
"Spectral Count"="Spectral Count"),
selected = "Intensity"),
),
conditionalPanel(
condition = "input.exp == 'TMT-peptide'",
fileInput('tmt_pept_expr', 'Upload peptide-level TMT-I report *.tsv',
accept=c('text/tsv',
'text/tab-separated-values,text/plain',
'.tsv')),
fileInput('tmt_pept_annot', 'Upload experimental design template/annotation',
accept=c('text/tsv',
'text/tab-separated-values,text/plain',
'.tsv'))
),
conditionalPanel(
condition = "input.exp == 'DIA-peptide'",
fileInput('dia_pept_expr', 'Upload DIA precursor report *.pr_matrix.tsv',
accept=c('text/tsv',
'text/tab-separated-values,text/plain',
'.tsv')),
fileInput('dia_pept_annot', 'Upload experimental design template/annotation',
accept=c('text/tsv',
'text/tab-separated-values,text/plain',
'.tsv'))
),
tags$hr(),
menuItem("Advanced Options",tabName="advanced", icon = icon("cogs"),
numericInput("min_global_appearance",
"Min percentage of non-missing values globally",
min = 0, max = 100, value = 0),
numericInput("min_appearance_each_condition",
"Min percentage of non-missing values in at least one condition",
min = 0, max = 100, value = 0),
numericInput("p",
"DE Adjusted p-value cutoff",
min = 0, max = 0.1, value = 0.05),
numericInput("lfc",
"DE Log2 fold change cutoff",
min = 0, max = 10, value = 1),
# checkboxInput("paired",
# "Paired test", FALSE),
radioButtons("normalization",
"Normalization type",
choices = c("No normalization"="none",
"Variance stabilizing normalization (LFQ and DIA only)"="vsn",
"Median centered"="MD"
), selected = "none"),
radioButtons("imputation",
"Imputation type",
choices = c("No imputation"="none", "Perseus-type"="man",
"MLE"="MLE", "knn"="knn", "bpca"="bpca"),
selected = "man"),
radioButtons("fdr_correction",
"Type of FDR correction",
choices = c("Benjamini Hochberg"="BH",
"Local and tail area-based"="fdrtool"
), selected= "BH")
# checkboxInput("s",
# "Paired test", FALSE),
# numericInput("k_number",
# "Number of clusters in heatmap",
# min = 1, max = 10, value = 3)
),
tags$hr(),
actionButton("analyze", "Run"),
#actionButton("load_data", "Load example data")
tags$script(HTML("
$(document).ready(function() {
$('#analyze').on('click', function(){$(this).blur()});
});
"))
)),
# convertMenuItem(menuItem('Demo', icon=icon("eye"), tabName = "demo"), tabName = "demo"),
convertMenuItem(
tabName = "info",
menuItem('Documentation', icon=icon("question"),
tabName = "info"))
)
), # sidebar close
################################################################
## DASHBOARD BODY
################################################################
dashboardBody(
useShinyjs(), #imp to use shinyjs functions
# comment out when testing on local
#tags$head(includeHTML(("google_analytics.html"))),
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "./css/custom.css")
),
tags$head(tags$script(HTML(
ifelse(DEBUG, '', '// Enable navigation prompt
window.onbeforeunload = function() {
return "Changes that you made may not be saved.";
};')
))),
# Add logo to the body
# tags$img(src="mbpf_logo.jpg",height=50, align="right"),
## Add tabItems
# id="body",
tabItems(
tabItem(tabName = "home",
fluidRow(
box(
title = "Overview",
width = 12,
solidHeader = TRUE,
status = "primary",
h3("BCM LysoProteomics-Analyst"),
p(HTML(paste0("BCM LysoProteomics-Analyst is an interactive web app to explore
differential expression analysis with “one click” and to visualize quantitative Lysosomal proteomic datasets analyzed using DIA-NN and Fragpipe.",
" BCM LysoProteomics-Analyst is built on the Monash ",
a(href="https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst/", target="_blank", "Analyst Suites"),
" SDK."))),
br(),
fluidRow(
column(width = 4,
h4("Features"),
tags$ul(
tags$li("Differential expression analysis"),
tags$li("Enrichment analysis (GO/Pathways)"),
tags$li("Imputation (optional)"),
tags$li("Data visualization"),
tags$ul(
tags$li("PCA"),
tags$li("Sample correlation"),
tags$li("Heatmaps"),
tags$li("Missing values inspection"),
tags$li("Sample coverage"),
tags$li("Protein intensity plots for selected protein(s)"),
tags$li("Imputation effect evaluation")
),
)
),
column(width = 8,
h4("Example Results"),
fluidRow(
style='margin: 0px;',
column(width = 6, box(width="100%", img(src="PCA_plot.png", style="width: 100%;"))),
column(width = 6, box(width="100%", img(src="heatmap.png", style="width: 100%;")))
)
)
),
br(),
fluidRow(
column(width = 4,
h4("Sidebar tabs"),
tags$ul(
tags$li(tags$b("Analysis: "),"upload your datasets")
# tags$li(tags$b("Demo: "),"familiarise yourself with FragPipe-Analyst by browsing through pre-analysed results"),
)
),
column(width = 8,
)
)
) # box 1 closed
) # fluidRow close
), # home tab close
tabItem(tabName = "analysis",
div(id="quickstart_info",
fluidPage(
box(
title = "Getting Started",
h3(tags$b(span("Running Datasets", style="text-decoration:underline"))),
tags$ul(
tags$li("Choose based on MS acquisition type."),
),
br(),
# HTML('<center><img src="./LFQ_analyst.svg" width="500px"></center>'),
width = 12,
solidHeader = TRUE,
status = "danger"
)
)
), # QUICKSTART INFO CLOSE
shinyjs::hidden(
div(id="panel_list",
tabsetPanel(id = "tab_panels",
type = "tabs",
selected = "LFQ-Analyst",
tabPanel("Quantification",
value = "quantification_panel",
br(),
fluidRow(
box(
column(6,uiOutput("downloadTable"),offset = 1),
column(4,uiOutput("downloadButton")), # make the button on same line
width = 4),
box(
column(12, uiOutput("significantBox")), width = 4
),
box(
column(5,uiOutput("downloadreport")), # offset for dist between buttons
#tags$br(),
#column(5,uiOutput('downloadPlots')),
width = 4),
), #close first fluidrow
# 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
## Data table and result plots box
fluidRow(id="results_tab",
tags$style(type="text/css",
".datatables.html-widget.html-widget-static-bound {
height: auto !important;
width: 90vw !important;
}
.dataTables_scrollBody {
height: unset !important;
max-height: none !important;
}"),
box(
title = "Results Table",
shinycssloaders::withSpinner(DTOutput("contents"),
color = "#3c8dbc"),
# actionButton("clear", "Deselect Rows"),
actionButton("original", "Refresh Table"),
width = 6,
status = "success",
#color=""
solidHeader = TRUE
),
# column(
box(
width = 6,
collapsible = F,
#status="primary",
#solidHeader=TRUE,
tabBox(
title = "Result Plots",
width = 12,
tabPanel(title = "Volcano plot",
fluidRow(
box(uiOutput("volcano_cntrst"), width = 5),
box(numericInput("fontsize",
"Font size",
min = 0, max = 8, value = 4),
width = 3),
box(checkboxInput("check_names",
"Display names",
value = T),
checkboxInput("p_adj",
"Adjusted p values",
value = T),
checkboxInput("show_gene",
"Show gene names",
value = T),
checkboxInput("disable_peptides",
"Don't color peptides from the same protein",
value = F),
width = 4),
),
fluidRow(
box(
tags$p("Select features from Results Table to highlight them on the plot"),
# OR drag the mouse on plot to show expression of features in Table
width = 12
)
),
fluidRow(
shinycssloaders::withSpinner(
plotOutput("volcano",
height = 600,
brush = "protein_brush" # click = "protein_click"
), color = "#3c8dbc"),
downloadButton('downloadVolcano', 'Save Highlighted Plot'),
actionButton("resetPlot", "Clear Selection")
)),
tabPanel(title= "Heatmap",
fluidRow(
box(checkboxInput("show_row_names",
"Show rownames",
value = F),
width = 6
)
),
fluidRow(
shinycssloaders::withSpinner(plotOutput("heatmap", height = 600), color = "#3c8dbc")
),
fluidRow(
# box(numericInput("cluster_number",
# "Cluster to download",
# min=1, max=6, value = 3), width = 6),
box(
# downloadButton('downloadCluster',"Save Cluster"),
downloadButton('download_hm_svg', "Save svg"),
width = 5)
),
# align save button
tags$style(type='text/css', "#downloadCluster {margin-top: 25px;}"),
tags$style(type='text/css', "#download_hm_svg {margin-top: 25px;}")
),
tabPanel(title = "Feature Plot",
fluidRow(
box(radioButtons("type",
"Plot type",
choices = c("Box Plot"= "boxplot",
"Violin Plot"="violin"),
selected = "boxplot",
inline = TRUE),
width = 6
),
box(checkboxInput("check_impute",
"Show imputed values",
value = F),
width = 6
)
),
fluidRow(
box(
tags$p("Select one or more rows from Results Table to plot individual
protein intesities across conditions and replicates"),
width = 12
)
),
fluidRow(
shinycssloaders::withSpinner(plotlyOutput("protein_plot"), color = "#3c8dbc")
# downloadButton('downloadProtein', 'Download Plot')
)
)
) # tabBox end
) # box or column end
), # result fluidRow close
## QC Box
fluidRow(
id="qc_tab",
box(width = 6,
tabBox(title = "QC Plots", width = 12, id="qc_tabBox", height=800,
tabPanel(title = "PCA Plot",
fluidRow(
column(6, checkboxInput("pca_imputed",
"Show imputed version",
value = F)),
column(6, checkboxInput("pca_scale",
"Show scaled version",
value = T))
),
fluidRow(shinycssloaders::withSpinner(plotlyOutput("pca_plot", height = 600), color = "#3c8dbc"))
),
tabPanel(title="Sample Correlation",
fluidRow(box(checkboxInput("cor_imputed",
"Show imputed version",
value = F),
width = 6
)),
fluidRow(shinycssloaders::withSpinner(plotOutput("sample_corr", height = 600), color = "#3c8dbc")),
fluidRow(downloadButton('download_corr_svg', "Save svg"))
),
tabPanel(title= "Sample CVs",
fluidRow(
box(checkboxInput("cvs_full_range",
"Show full range",
value = F),
width = 6
)
),
fluidRow(
shinycssloaders::withSpinner(plotOutput("sample_cvs", height = 600), color = "#3c8dbc")
),
fluidRow(
downloadButton('download_cvs_svg', "Save svg")
)),
tabPanel(title = "Feature Numbers",
shinycssloaders::withSpinner(plotOutput("numbers", height = 600), color = "#3c8dbc"),
downloadButton('download_num_svg', "Save svg")),
tabPanel(title = "Sample coverage", value="sample_coverage_tab",
shinycssloaders::withSpinner(plotOutput("coverage", height = 600), color = "#3c8dbc"),
downloadButton('download_cov_svg', "Save svg")),
tabPanel(title = "Missing values - Heatmap", value="missingval_heatmap_tab",
shinycssloaders::withSpinner(plotOutput("missval", height = 600), color = "#3c8dbc"),
downloadButton('download_missval_svg', "Save svg")
),
tabPanel(title = "Density plot", value="density_tab",
shinycssloaders::withSpinner(plotOutput("density", height = 600), color = "#3c8dbc"),
downloadButton('download_density_svg', "Save svg")
)
# ,
# tabPanel(title = "p-value Histogram",
# plotOutput("p_hist", height = 600)
# )
) # Tab box close
),
box(
width=6,
tabBox(title = "Enrichment", width = 12, height=800,
tabPanel(title= "Pathway enrichment",
fluidRow(
column(4,uiOutput("contrast_1")),
column(4, selectInput("pathway_database", "Pathway database:",
c("Hallmark"="MSigDB_Hallmark_2020",
"KEGG"="KEGG_2021_Human",
"Reactome"="Reactome_2022",
"WikiPathways"="WikiPathway_2023_Human",
"KEGG (Mouse)"="KEGG_2019_Mouse",
"WikiPathways (Mouse)"="WikiPathways_2019_Mouse"))),
column(3, radioButtons("pathway_direction",
"Direction",
choices = c("Up"="UP", "Down"="DOWN"),
inline = T,
selected = "UP")),
column(1, shinyWidgets::dropdownButton(
circle = TRUE, status = "default", right = T,
icon = icon("gear"), width = "300px",
numericInput("p_path",
"DE adjusted p-value cutoff",
min = 0, max = 1, value = 0.05),
numericInput("lfc_path",
"DE log2 fold change cutoff",
min = 0, max = 10, value = 1),
checkboxInput("path_adjust",
"Use adjusted p-value",
value = F),
checkboxInput("pathway_whole_proteome",
"Whole proteome as background",
value = T),
tooltip = tooltipOptions(placement="left",
title = "customize settings"))
)
),
fluidRow(
column(4, actionButton("pathway_analysis", "Run Enrichment")),
column(6, tags$p("Note: Currently, only human (default) and mouse data are supported."))
),
fluidRow(box(width = 12, uiOutput("spinner_pa"), height = 500)),
fluidRow(column(12, downloadButton('downloadPA', 'Download Table')))
),
tabPanel(title="Gene Ontology",
fluidRow(
column(4, uiOutput("contrast")),
column(4, selectInput("go_database", "GO database:",
c("Molecular Function"="GO_Molecular_Function_2021",
"Cellular Component"="GO_Cellular_Component_2021",
"Biological Process"="GO_Biological_Process_2021"))),
column(3, radioButtons("go_direction",
"Direction",
choices = c("Up"="UP", "Down"="DOWN"),
inline=T,
selected = "UP")),
column(1, shinyWidgets::dropdownButton(
circle = TRUE, status = "default", right = T,
icon = icon("gear"), width = "300px",
numericInput("p_go",
"DE adjusted p-value cutoff",
min = 0, max = 1, value = 0.05),
numericInput("lfc_go",
"DE log2 fold change cutoff",
min = 0, max = 10, value = 1),
checkboxInput("go_adjust",
"Use adjusted p-value",
value = F),
checkboxInput("go_whole_proteome",
"Whole proteome as background",
value = T),
tooltip = tooltipOptions(placement="left",
title = "customize settings")
))
),
fluidRow(
column(4, actionButton("go_analysis", "Run Enrichment")),
column(6, tags$p("Note: Currently, only human data is supported"))
),
fluidRow(box(width = 12, uiOutput("spinner_go"), height = 500)),
fluidRow(column(12, downloadButton('downloadGO', 'Download Table')))
)
) # Tab box close
) # box end
) # fluidrow qc close
),# lfq-analyst panel close
tabPanel('Absence/Presence',
value = "occ_panel",
br(),
fluidRow(
tags$style(
".box {
border-top: none;
box-shadow: 0 0px 0px rgb(0 0 0 / 10%);
}"
),
column(3,
box(width =NULL,
title = "Filter Options",
tags$p("Filtering your identification result based on predeefined filter conditions,
and/or changing the sliders of each condition below"),
br(),
div(id = "venn_filter",
tags$h4("Subset Results Table"),
shinyWidgets::prettyCheckboxGroup("filtered_condition_fragpipe",
"Filters",
choices = c('Proteins with more than two peptides'),
shape = "round",
selected = NULL)
),
tags$hr(),
tags$h4("Number of samples present"),
tags$style(type = "text/css", ".irs-grid-pol.small {height: 0px;}"), # hide minor ticks of a sliderInput
uiOutput('sidebar'),
status = "success",
solidHeader = TRUE)
), # slider bar column closed
column(9,
box(width = NULL,
collapsible = T,
title = "Filtered Results Table",
shinycssloaders::withSpinner(DT::dataTableOutput("contents_occ"), color = "#3c8dbc"),
downloadButton('download_attendance', 'Download Table'),
status = "success",
solidHeader = TRUE),
tabBox(
width = NULL,
height = 640,
tabPanel(
title = "Venn Plot",
tags$p('Select conditions/groups to generate the Venn plot. By default, more than three conditions/groups generates a 3D Venn plot,
set Condition 3 as "NONE" to generate a 2D Venn plot'),
column(12,
box(width = 4,id = "con_1",uiOutput("condition_1")),
box(width = 4,id = "con_2", uiOutput("condition_2")),
box(width = 4,id = "con_3", uiOutput("condition_3"))),
column(12,
shinycssloaders::withSpinner(plotOutput("venn_plot"), color = "#3c8dbc")),
downloadButton('download_venn_svg', "Save svg")
),
tabPanel(
title = "UpSet Plot",
shinycssloaders::withSpinner(plotOutput("upset_plot",width = "100%", height = 540),
color = "#bec8da"),
downloadButton('download_upset_svg', "Save svg")
),
tabPanel(
title = "Jaccard Similarity",
shinycssloaders::withSpinner(plotOutput("Jaccard",width = "100%", height = 540),
color = "#bec8da")
)
)
# box(width = NULL,
# title = "Venn Plot",
# tags$p('Select conditions/groups to generate the Venn plot. By default, more than three conditions/groups generates a 3D Venn plot,
# set Condition 3 as "NONE" to generate a 2D Venn plot'),
# column(12,
# box(width = 4,id = "con_1",uiOutput("condition_1")),
# box(width = 4,id = "con_2", uiOutput("condition_2")),
# box(width = 4,id = "con_3", uiOutput("condition_3"))),
# column(12,
# shinycssloaders::withSpinner(plotOutput("venn_plot"), color = "#3c8dbc")),
# column(12, downloadButton('download_venn_svg', "Save svg")),
# status = "success",
# solidHeader = TRUE)
) # Venn plot column closed
) # fuildRow closed
) # occurrence panel closed
) # panel_list close
) # div close
#bookmarkButton()
)), #analysis tab close
tabItem(tabName = "info",
fluidRow(
box(
title = "Documentation",
h3("Documents and Vigenettes for analysis"),
tags$ul(
tags$li("Documentation coming soon!")
),
width = 12,
solidHeader = TRUE,
status = "primary"
)
)
)# info tab close
# , tabItem(tabName = "demo",
# div(id="downloadbox_dm",
# fluidRow(
# box(
# column(6,uiOutput("downloadTable_dm"),offset = 1),
# column(4,uiOutput("downloadButton_dm")), # make the button on same line
# width = 4),
#
# infoBoxOutput("significantBox_dm",width = 4),
# box(
# column(5,uiOutput("downloadreport_dm")), # offset for dist between buttons
# #tags$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)),
# conditionalPanel(condition="input.exp != 'TMT'",
# tabPanel(title = "Protein Numbers",
# plotOutput("numbers_dm", height = 600))),
# conditionalPanel(condition="input.exp != 'TMT'",
# 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", height=600),
# downloadButton('downloadGO_dm', 'Download Table'),
# height=600
# ),
# 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", height=600),
# downloadButton('downloadPA_dm', 'Download Table'),
# height=600
# ) #### Tab demo closed
#
# ) # Tab box close
# ))) # fluidrow qc close
# ) # Tab items close
),
fluidRow(
tags$div(
tags$footer(
tags$p(" "),
align = "left",
style = "margin-left: 20px;")
# style = "position:absolute;
# bottom:0;
# width:100%;
# height:50px; /* Height of the footer */")
),
shiny.info::version(position = "bottom left")
)
) # Dasbboardbody close
) #Dashboard page close
)#Shiny U Close
}