inst/shiny-examples/myapp/ui.R
In lagelab/Genoppi: genoppi
body <- dashboardBody(
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "custom.css")
),
fluidRow(
tabItems(
tabItem(tabName = "dashboard",
shinyjs::useShinyjs(),
tabsetPanel(id = "basic", #width = 12,
tabPanel("Basic plotting", id = 'basicplot', value = "p1",
br(),
column(width = 4,
box(
title = "Basic plot options", width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = FALSE,
fluidRow(
column(12, uiOutput('a_select_scatterplot_ui'))
),
fluidRow(
column(6, uiOutput("a_color_theme_indv_sig")),
column(6, uiOutput("a_color_theme_indv_insig"))
)
),
box(
title = "Summary", width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = FALSE,
fluidRow(
column(12, uiOutput("VP_count_text")),
br(),
),
fluidRow(
column(12, tableOutput("a_verbatim_count_ui")),
br()
),
fluidRow(
br(),
column(12, uiOutput('a_replicate_summar_text_ui')),
),
fluidRow(
column(12, tableOutput("a_replicate_summary_table_ui"))
),
br(),
fluidRow(
column(12, uiOutput("a_monitor_pulldown_ui"))
),
fluidRow(
column(12, uiOutput("a_monitor_pulldown_mapping_ui"))
),
fluidRow(
br(),
column(12, shinyjs::hidden(myDownloadButton("a_mttest_mapping_download", 'Proteomic data', icon("download"))))
)
)#,
#shinyjs::hidden(box( #
# id='box_mapping_warning_ui', title = "Error!", width = NULL, solidHeader = TRUE, status = "warning", collapsible = TRUE, collapsed = FALSE,
# fluidRow(
# column(12, uiOutput('a_in_pulldown_check_ui'))
# )
#))
),
column(width = 8,
box(
title = tagList(shiny::icon('chart-area'), "Volcano plot"), width = NULL, solidHeader = TRUE, status = 'success', collapsible = TRUE,
fluidRow(
column(11, shinyjs::hidden(myDownloadButton("a_volcano_plot_download", 'Volcano plot')))
),
fluidRow(style = "padding-bottom:75px",
#column(1, plotOutput("FDR_colorbar", width = "50px")),
column(12, shinycssloaders::withSpinner(plotlyOutput("VolcanoPlot"), spinner_type)) #, width = "550px", height = "550px"
),
),
box(
title = tagList(img(src='icon_scatter.png',width='22px'), "Scatter plot"), width = NULL, solidHeader = TRUE, status = 'success', collapsible = TRUE, collapsed = FALSE,
fluidRow(
column(11, shinyjs::hidden(myDownloadButton("a_scatter_plot_download", 'Scatter plot')))
),
fluidRow(style = "padding-bottom:75px",
column(11, shinycssloaders::withSpinner(plotlyOutput("ScatterPlot"), spinner_type)) #, width = "550px", height = "550px"
)
)
)
),
tabPanel("Integrated plotting", id = 'integratedplot', value = "p2",
br(),
column(width = 4,
box(
title = "InWeb / iRefIndex / BioPlex", width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = FALSE, # tagList(img(src='icon_inweb.png',width='20px'),
fluidRow(
column(12,
uiOutput("a_ppi_select_ui"))
),
# InWeb
fluidRow(
column(8, uiOutput("a_bait_layer")),
column(4,
uiOutput("a_inweb_type"),
uiOutput("a_irefindex_type_ui"),
uiOutput("a_bioplex_type_ui")
)
),
# footer
fluidRow(
column(4, uiOutput("a_overlay_inweb_ui"), uiOutput("a_ppi_message")),
column(4, uiOutput("a_label_inweb_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_ppi_mapping_df_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
),
fluidRow(
column(12, uiOutput("info_inweb_ui"))
)
),
box(
title = "GWAS catalog", width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = TRUE,
fluidRow(
column(12, uiOutput('a_gwas_catalogue_ui'))
),
fluidRow(
column(4, uiOutput("a_overlay_gwas_cat_ui")),
column(4, uiOutput("a_label_gwas_cat_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_gwas_catalogue_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
),
fluidRow(
column(12, uiOutput('a_gwas_subset_traits_by_data'))
#column(6, uiOutput('a_gwas_subset_traits_by_data_freq'))
),
fluidRow(
column(12, uiOutput("info_gwas_ui"))
)
),
box(
title = tagList('gnomAD'), width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = TRUE,
fluidRow(
#column(4,uiOutput('a_select_gnomad_pli_type_ui')),
column(12,
uiOutput('a_slide_gnomad_pli_threshold_ui'),
uiOutput('a_gnomad_colorscale_text_ui'),
#plotOutput('a_gnomad_colorscale_ui', width = "275px", height = '100px')
)
),
fluidRow(
column(4, uiOutput("a_overlay_gnomad_ui")),
column(4, uiOutput("a_label_gnomad_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_gnomad_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
),
fluidRow(
column(12, uiOutput("info_gnomad_ui"))
)
#fluidRow(column(12, uiOutput('a_gnomad_constraints_available_ui'))),
#fluidRow(column(12, tableOutput("a_table_gnomad_constraints_ui")))
),
box(
title = "GTEx / HPA", width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = TRUE,
fluidRow(
column(12, uiOutput('a_tissue_select_ui'),
uiOutput("a_gtex_rna_tissue_ui"),
uiOutput("a_gtex_protein_tissue_ui"),
uiOutput("a_hpa_rna_tissue_ui")),
),
fluidRow(
column(4, uiOutput("a_overlay_tissue_ui")),
column(4, uiOutput("a_label_tissue_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_tissue_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
),
fluidRow(
column(12, uiOutput("info_tissue_ui"))
)
),
box(
title ='Upload SNPs', width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = TRUE,
fluidRow(
column(12, uiOutput("a_SNP_file"))
),
fluidRow(
column(4, uiOutput("a_overlay_snp_ui")),
column(4, uiOutput("a_label_snp_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_snp_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
)
),
box(
title = "Upload genes", width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = TRUE,
fluidRow(
column(12, uiOutput("a_genes_file")),
),
fluidRow(
column(4, uiOutput("a_overlay_genes_upload_ui")),
column(4, uiOutput("a_label_genes_upload_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_gene_upload_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
)
),
box(
title = "Settings", width = NULL, solidHeader = TRUE, collapsible = TRUE, collapsed = FALSE,
fluidRow(
column(3, align = 'left', h5(strong('Overlay'))),
column(3, align = 'center', h5(strong(uiOutput("a_sig_text_ui")))),
column(3, align = 'center', h5(strong(uiOutput("a_insig_text_ui")))),
column(3, align = 'center', h5(strong('Symbol'))),
),
#fluidRow(column(12, h5('InWeb'))),
fluidRow(
column(3, h5('InWeb / iRefIndex / BioPlex')),
column(3, uiOutput("a_color_inweb_sig_ui")),
column(3, uiOutput("a_color_inweb_insig_ui")),
column(3, uiOutput("a_symbol_inweb_ui"))
),
#fluidRow(column(12, h5('GWAS catalogue'))),
fluidRow(
column(3, h5('GWAS catalog')),
column(3, uiOutput("a_color_gwas_cat_sig_ui")),
column(3, uiOutput("a_color_gwas_cat_insig_ui")),
column(3, uiOutput("a_symbol_gwas_cat_ui"))
),
#fluidRow(column(12, h5('gnomAD'))),
fluidRow(
column(3, h5('gnomAD')),
column(3, uiOutput("a_color_gnomad_sig_ui")),
column(3, uiOutput("a_color_gnomad_insig_ui")),
column(3, uiOutput("a_symbol_gnomad_ui"))
),
fluidRow(
column(3, h5('GTEx / HPA')),
column(3, uiOutput("a_color_tissue_sig_ui")),
column(3, uiOutput("a_color_tissue_insig_ui")),
column(3, uiOutput("a_symbol_tissue_ui"))
),
#fluidRow(column(12, h5('SNPs upload'))),
fluidRow(
column(3, h5('SNPs upload')),
column(3, uiOutput("a_color_snp_sig_ui")),
column(3, uiOutput("a_color_snp_insig_ui")),
column(3, uiOutput("a_symbol_snp_ui"))
),
#fluidRow(column(12, h5('genes upload'))),
fluidRow(
column(3, h5('Genes upload')),
column(3, uiOutput("a_color_genes_upload_sig_ui")),
column(3, uiOutput("a_color_genes_upload_insig_ui")),
column(3, uiOutput("a_symbol_genes_upload_ui"))
)
)
),
column(width = 8,
box(
title = tagList(shiny::icon('chart-area'), "Volcano plot"), solidHeader = TRUE, status = 'success', collapsible = TRUE, width = 12,
# height = '800px'
fluidRow(
column(12, shinyjs::hidden(myDownloadButton("a_integrated_plot_download",'Volcano plot')))
),
fluidRow(style = "padding-bottom:150px",
column(12, shinycssloaders::withSpinner(plotlyOutput("Multi_VolcanoPlot"), spinner_type)),
)
),
tabBox(
title = tagList(img(src='icon_venn_a.png',width='22px'), 'Venn diagrams'), width = 12, #status = 'success', collapsible = TRUE,
tabPanel('InWeb / iRefIndex / BioPlex',
fluidRow(
column(4, plotOutput('a_inweb_venn_ui', width = "220px", height = "220px")),
column(5, br(), br(), br(), br(), uiOutput("a_ppi_venn_verbatim_ui")),
column(3, shinyjs::hidden(myDownloadButton("a_inweb_venn_mapping_download", 'Genes', icon("download"))))
),
),
tabPanel('GWAS catalog',
fluidRow(
column(4, plotOutput('a_gwas_catalogue_venn_all_ui', width = "220px", height = "220px")),
column(5, br(), br(), br(), br(), uiOutput('a_gwas_catalogue_venn_verbatim_ui')),
column(3, shinyjs::hidden(myDownloadButton("a_gwas_catalogue_venn_mapping_download", 'Genes', icon("download"))))
),
),
tabPanel('gnomAD',
fluidRow(
column(4, plotOutput('a_gnomad_venn_ui', width = "220px", height = "220px")),
column(5, br(), br(), br(), br(), uiOutput("a_gnomad_venn_verbatim_ui")),
column(3, shinyjs::hidden(myDownloadButton("a_gnomad_venn_mapping_download", 'Genes', icon("download"))))
)
),
tabPanel('GTEx / HPA',
fluidRow(
column(4, plotOutput('a_tissue_venn_ui', width = "220px", height = "220px")),
column(5, br(), br(), br(), br(), uiOutput("a_tissue_venn_verbatim_ui")),
column(3, shinyjs::hidden(myDownloadButton("a_tissue_venn_mapping_download", 'Genes', icon("download"))))
),
),
tabPanel('SNPs upload',
fluidRow(
column(4, plotOutput('a_snp_venn_ui', width = "220px", height = "220px")),
column(5, br(), br(), br(), br(),
uiOutput('a_snp_venn_verbatim_ui')),
column(3, uiOutput('a_select_venn_snp_ui'),
uiOutput('a_select_venn_snp_loci_ui'),
shinyjs::hidden(myDownloadButton("a_snp_venn_mapping_download", 'Genes', icon("download"))))
)
),
tabPanel('Genes upload',
fluidRow(
column(4, plotOutput('a_genes_upload_venn_ui', width = "220px", height = "220px")),
column(5, br(), br(), br(), br(),
uiOutput('a_genes_upload_venn_verbatim_ui')),
column(3, uiOutput('a_select_venn_genes_upload_ui'),
shinyjs::hidden(myDownloadButton("a_genes_upload_venn_mapping_download", 'Genes', icon("download")))),
),
)
)
)
),
tabPanel("Gene set annotations", value = "p4",
br(),
column(4,
box(
title = tagList("Settings"), width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE,
fluidRow(
column(12, uiOutput("a_pf_loc_selection")),
),
fluidRow(
column(12, uiOutput("a_pathway_mapping_freq_slider_ui"))
),
fluidRow(
column(12, uiOutput("a_pathway_mapping_search_ui"))
),
fluidRow(
column(12, uiOutput("a_pathway_mapping_type_sort_ui"))
),
fluidRow(
column(8,''),
column(4, shinyjs::hidden(myDownloadButton("a_pathway_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
),
fluidRow(
column(12, uiOutput("info_geneset_ui"))
)
)
),
column(8,
box(
title = tagList(shiny::icon('chart-area'), "Volcano plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
fluidRow(
column(3, shinyjs::hidden(myDownloadButton("a_pathway_plot_download", 'Volcano plot'))),
column(3, shinyjs::hidden(myDownloadButton("a_pathway_plot_legend_download", 'Volcano plot (legend)'))),
column(6, '')
),
fluidRow(style = "padding-bottom:125px",
column(12, shinycssloaders::withSpinner(plotlyOutput('VolcanoPlotPathway'), spinner_type))
)
),
box(
title = tagList("Annotation table"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
fluidRow(
column(12, DT::dataTableOutput('a_pathway_data_table_ui'))
)
)
)
),
tabPanel("Tissue enrichment", value = "p4",
br(),
column(4,
box(
title = tagList('Settings'), width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE,
fluidRow(
column(12,
uiOutput('a_tissue_select_source_ui'),
uiOutput('a_tissue_enrichment_upload_ui'),
uiOutput('a_tissue_enrichment_type_select_ui'),
uiOutput('a_tissue_enrichment_slider_ui'),
uiOutput('a_tissue_enrichment_xaxis_ui'),
uiOutput('a_tissue_enrichment_scientific_notation_ui')
)
),
fluidRow(
column(6, uiOutput("a_button_plot_tissue_enrichment_ui")),
column(6, shinyjs::hidden(myDownloadButton("a_tissue_enrichment_download",'Tissue enrichment', img=icon('file-alt', lib = "font-awesome"))))
),
fluidRow(
column(12, uiOutput("info_tissue_enrichment_ui"))
)
)
),
column(8,
box(
title = tagList('Enrichment bar plot'), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE, height = 1000,
fluidRow(
column(12,
shinycssloaders::withSpinner(plotlyOutput('a_tissue_enrichment_ui'), spinner_type)
)
)
)
)
),
tabPanel("Inspect uploaded data (dev)", value = "p5",
fluidRow(
column(12,
DT::dataTableOutput('a_file_display_table_ui')
)
)
)
)
),
tabItem(tabName = "widgets",
shinyjs::useShinyjs(),
tabsetPanel(id = "comparison",
tabPanel("Basic plotting",
br(),
column(4,
box(
title = 'Settings for file 1', width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE,
column(12,
fluidRow(
column(6,
uiOutput("b_file_1_significance_type_ui"),
uiOutput("b_file_1_FDR_thresh"),
uiOutput("b_file_1_PVal_thresh")
),
column(6,
uiOutput('b_file_1_logfc_direction_ui'),
uiOutput("b_file_1_logFC_thresh")
)
),
fluidRow(
uiOutput('b_file_1_select_scatterplot_ui')
)
)
),
box(
title = 'Summary for file 1', width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE, collapsed = TRUE,
column(12,
fluidRow(
column(12,
uiOutput("b_file_1_summary_text_ui")
),
column(12,
tableOutput('b_file_1_summary_table_ui')
),
column(12,
shinyjs::hidden(myDownloadButton("b_file_1_mapping_download", 'Proteomic data', icon("download"))))
)
)
),
box(
title = tagList(shiny::icon('chart-area'), "Volcano plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
column(12,
fluidRow(
column(12, shinyjs::hidden(myDownloadButton("b_file_1_volcano_download", 'Volcano plot')))
),
fluidRow(
shinycssloaders::withSpinner(plotlyOutput('b_file_1_volcano'), spinner_type),
)
)
),
box(
title = tagList(img(src='icon_scatter.png',width='22px'), "Scatter plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE, collapsed = TRUE,
column(12,
fluidRow(
column(12, shinyjs::hidden(myDownloadButton("b_file_1_scatter_download", 'Scatter plot')))
),
fluidRow(
shinycssloaders::withSpinner(plotlyOutput('b_file_1_scatter'), spinner_type),
)
)
)
),
column(4,
box(
title = 'Settings for file 2', width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE,
column(12,
fluidRow(
column(6,
uiOutput("b_file_2_significance_type_ui"),
uiOutput("b_file_2_FDR_thresh"),
uiOutput("b_file_2_PVal_thresh")
),
column(6,
uiOutput('b_file_2_logfc_direction_ui'),
uiOutput("b_file_2_logFC_thresh")
)
),
fluidRow(
uiOutput('b_file_2_select_scatterplot_ui')
)
)
),
box(
title = 'Summary for file 2', width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE, collapsed = TRUE,
column(12,
fluidRow(
column(12,
uiOutput("b_file_2_summary_text_ui")
),
column(12,
tableOutput('b_file_2_summary_table_ui')
),
column(12,
shinyjs::hidden(myDownloadButton("b_file_2_mapping_download", 'Proteomic data', icon("download")))
)
)
)
),
box(
title = tagList(shiny::icon('chart-area'), "Volcano plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
column(12,
fluidRow(
column(12, shinyjs::hidden(myDownloadButton("b_file_2_volcano_download", 'Volcano plot')))
),
fluidRow(
shinycssloaders::withSpinner(plotlyOutput('b_file_2_volcano'), spinner_type),
)
)
),
box(
title = tagList(img(src='icon_scatter.png',width='22px'), "Scatter plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE, collapsed = TRUE,
column(12,
fluidRow(
column(12, shinyjs::hidden(myDownloadButton("b_file_2_scatter_download", 'Scatter plot')))
),
fluidRow(
shinycssloaders::withSpinner(plotlyOutput('b_file_2_scatter'), spinner_type),
)
)
)
),
column(4,
box(
title = 'Settings for file 3', width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE,
column(12,
fluidRow(
column(6,
uiOutput("b_file_3_significance_type_ui"),
uiOutput("b_file_3_FDR_thresh"),
uiOutput("b_file_3_PVal_thresh")
),
column(6,
uiOutput('b_file_3_logfc_direction_ui'),
uiOutput("b_file_3_logFC_thresh")
)
),
fluidRow(
uiOutput('b_file_3_select_scatterplot_ui')
)
)
),
box(
title = 'Summary for file 3', width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE, collapsed = TRUE,
column(12,
fluidRow(
column(12,
uiOutput("b_file_3_summary_text_ui")
),
column(12,
tableOutput('b_file_3_summary_table_ui')
),
column(12,
shinyjs::hidden(myDownloadButton("b_file_3_mapping_download", 'Proteomic data', icon("download")))
)
)
)
),
box(
title = tagList(shiny::icon('chart-area'), "Volcano plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
column(12,
fluidRow(
column(12, shinyjs::hidden(myDownloadButton("b_file_3_volcano_download", 'Volcano plot')))
),
fluidRow(
shinycssloaders::withSpinner(plotlyOutput('b_file_3_volcano'), spinner_type),
)
)
),
box(
title = tagList(img(src='icon_scatter.png',width='22px'), "Scatter plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE, collapsed = TRUE,
column(12,
fluidRow(
column(12, shinyjs::hidden(myDownloadButton("b_file_3_scatter_download", 'Scatter plot')))
),
fluidRow(
shinycssloaders::withSpinner(plotlyOutput('b_file_3_scatter'), spinner_type),
)
)
)
)
),
tabPanel("Venn diagrams",
br(),
column(6,
box(
title = tagList(img(src='icon_venn_a.png',width='22px'), 'Venn diagrams'), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE, collapsed = TRUE,
column(1, ''),
column(8,
fluidRow(
plotOutput('b_file_comparison_venn_ui', width = "280px", height = "280px")
),
fluidRow(
uiOutput('b_file_comparison_venn_verbatim_ui')
)
),
column(3, '')
),
box(
title = 'Venn diagram explanations', width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
column(12,
fluidRow(
uiOutput('b_file_comparison_venn_explanations_ui')
)
)
)
),
column(6,
box(
title = 'Explore overlap', width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE, collapsed = TRUE,
fluidRow(
column(4,
uiOutput('b_file_comparison_data_table_select_ui')
),
column(4,
myDownloadButton("b_file_comparison_data_table_download_ui", 'Genes', icon("download"))
),
column(4,
''
)
),
fluidRow(
column(12,
DT::dataTableOutput('b_file_comparison_data_table_ui')
)
)
)
)
)
)
),
tabItem(tabName = "guide",
# works in browser format
tags$iframe(src = "welcome_guide_v1.0_210514.pdf",
style="width:100%;", #frameborder="0"
height = "3100px")
),
tabItem(tabName = "start",
fluidRow(
column(3, ''),
column(6,
# top of table
fluidRow(style = "padding-top:200px",
column(12, align = 'center',
h1(strong("Genoppi"), style = "font-size:100px;"),
br(),
uiOutput('a_example_file_ui'),
uiOutput('a_get_example_file_ui')
)
),
fluidRow(
br(),
h5(HTML(paste('<b>Genoppi</b> is an open-source software for performing quality control and
analyzing quantitative proteomic data. Genoppi streamlines the integration of
proteomic data with external datasets such as known protein-protein interactions
in published literature, data from genetic studies, gene set annotations, or other
user-defined inputs. See the', actionLink('tab_welcome','welcome guide'),
'for more details.') ))
),
fluidRow(style = "padding-top:300px",
column(12, align = 'center',
h6(HTML(paste0(actionLink('enable_dev_mode', 'Developer mode'))))
)
),
),
column(3, '')
)
),
tabItem(tabName = "documentation",
fluidRow(
column(1, ''),
column(10,
# top of table
fluidRow(style = "padding-top:100px",
column(12, align = 'left',
h1(strong("Data documentation"), style = "font-size:30px;"),
br(),
uiOutput('documentation_ui')
)
)
),
column(1, '')
)
)
)
)
)
sidebar <- dashboardSidebar(
sidebarMenu(id = "sidebarmenu",
#h6(as.character(genoppi.ver)),
menuItem("Quick Start", tabName = "start", icon = icon("stream")),
menuItem("Guide", tabName = "guide", icon = icon("info-circle")),
menuItem("Data Documentation", icon = icon("question-circle"), tabName = "documentation", badgeLabel = "new", badgeColor = "green"),
menuItem("Single File", tabName = "dashboard", icon = icon("file")),
menuItem("Multi Files Comparison", icon = icon("copy"), tabName = "widgets"),
conditionalPanel("input.sidebarmenu === 'dashboard'",
uiOutput("a_file"),
uiOutput("a_in_pulldown_check_ui"),
#uiOutput('a_make_example_file'),
HTML('<hr style="border-color: #D6DBE0;">'),
uiOutput("a_bait_search"),
uiOutput("a_GOI_search"),
uiOutput("a_GOI_search_alpha"),
#uiOutput("a_color_scheme"),
uiOutput("a_color_style"),
uiOutput("a_file_color"),
uiOutput("a_significance_type_ui"),
uiOutput("FDR_thresh"),
uiOutput("PVal_thresh"),
uiOutput('a_logfc_direction_ui'),
uiOutput("logFC_thresh")
),
conditionalPanel("input.sidebarmenu == 'widgets'",
uiOutput("b_file_1_ui"),
uiOutput("b_file_2_ui"),
uiOutput("b_file_3_ui"),
HTML('<hr style="border-color: #D6DBE0;">'),
uiOutput("b_GOI_search"),
uiOutput("b_GOI_search_alpha")
),
br(),
tags$footer(
tags$p(paste('version',genoppi.ver), style = "color: grey; text-align: center;")
)
)
)
# Put them together into a dashboardPage
dashboardPage(skin = "black",
#header,
dashboardHeader(title = 'Genoppi'),
sidebar,
body
)
lagelab/Genoppi documentation built on Oct. 13, 2022, 2:36 p.m.
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body <- dashboardBody(
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "custom.css")
),
fluidRow(
tabItems(
tabItem(tabName = "dashboard",
shinyjs::useShinyjs(),
tabsetPanel(id = "basic", #width = 12,
tabPanel("Basic plotting", id = 'basicplot', value = "p1",
br(),
column(width = 4,
box(
title = "Basic plot options", width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = FALSE,
fluidRow(
column(12, uiOutput('a_select_scatterplot_ui'))
),
fluidRow(
column(6, uiOutput("a_color_theme_indv_sig")),
column(6, uiOutput("a_color_theme_indv_insig"))
)
),
box(
title = "Summary", width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = FALSE,
fluidRow(
column(12, uiOutput("VP_count_text")),
br(),
),
fluidRow(
column(12, tableOutput("a_verbatim_count_ui")),
br()
),
fluidRow(
br(),
column(12, uiOutput('a_replicate_summar_text_ui')),
),
fluidRow(
column(12, tableOutput("a_replicate_summary_table_ui"))
),
br(),
fluidRow(
column(12, uiOutput("a_monitor_pulldown_ui"))
),
fluidRow(
column(12, uiOutput("a_monitor_pulldown_mapping_ui"))
),
fluidRow(
br(),
column(12, shinyjs::hidden(myDownloadButton("a_mttest_mapping_download", 'Proteomic data', icon("download"))))
)
)#,
#shinyjs::hidden(box( #
# id='box_mapping_warning_ui', title = "Error!", width = NULL, solidHeader = TRUE, status = "warning", collapsible = TRUE, collapsed = FALSE,
# fluidRow(
# column(12, uiOutput('a_in_pulldown_check_ui'))
# )
#))
),
column(width = 8,
box(
title = tagList(shiny::icon('chart-area'), "Volcano plot"), width = NULL, solidHeader = TRUE, status = 'success', collapsible = TRUE,
fluidRow(
column(11, shinyjs::hidden(myDownloadButton("a_volcano_plot_download", 'Volcano plot')))
),
fluidRow(style = "padding-bottom:75px",
#column(1, plotOutput("FDR_colorbar", width = "50px")),
column(12, shinycssloaders::withSpinner(plotlyOutput("VolcanoPlot"), spinner_type)) #, width = "550px", height = "550px"
),
),
box(
title = tagList(img(src='icon_scatter.png',width='22px'), "Scatter plot"), width = NULL, solidHeader = TRUE, status = 'success', collapsible = TRUE, collapsed = FALSE,
fluidRow(
column(11, shinyjs::hidden(myDownloadButton("a_scatter_plot_download", 'Scatter plot')))
),
fluidRow(style = "padding-bottom:75px",
column(11, shinycssloaders::withSpinner(plotlyOutput("ScatterPlot"), spinner_type)) #, width = "550px", height = "550px"
)
)
)
),
tabPanel("Integrated plotting", id = 'integratedplot', value = "p2",
br(),
column(width = 4,
box(
title = "InWeb / iRefIndex / BioPlex", width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = FALSE, # tagList(img(src='icon_inweb.png',width='20px'),
fluidRow(
column(12,
uiOutput("a_ppi_select_ui"))
),
# InWeb
fluidRow(
column(8, uiOutput("a_bait_layer")),
column(4,
uiOutput("a_inweb_type"),
uiOutput("a_irefindex_type_ui"),
uiOutput("a_bioplex_type_ui")
)
),
# footer
fluidRow(
column(4, uiOutput("a_overlay_inweb_ui"), uiOutput("a_ppi_message")),
column(4, uiOutput("a_label_inweb_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_ppi_mapping_df_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
),
fluidRow(
column(12, uiOutput("info_inweb_ui"))
)
),
box(
title = "GWAS catalog", width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = TRUE,
fluidRow(
column(12, uiOutput('a_gwas_catalogue_ui'))
),
fluidRow(
column(4, uiOutput("a_overlay_gwas_cat_ui")),
column(4, uiOutput("a_label_gwas_cat_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_gwas_catalogue_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
),
fluidRow(
column(12, uiOutput('a_gwas_subset_traits_by_data'))
#column(6, uiOutput('a_gwas_subset_traits_by_data_freq'))
),
fluidRow(
column(12, uiOutput("info_gwas_ui"))
)
),
box(
title = tagList('gnomAD'), width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = TRUE,
fluidRow(
#column(4,uiOutput('a_select_gnomad_pli_type_ui')),
column(12,
uiOutput('a_slide_gnomad_pli_threshold_ui'),
uiOutput('a_gnomad_colorscale_text_ui'),
#plotOutput('a_gnomad_colorscale_ui', width = "275px", height = '100px')
)
),
fluidRow(
column(4, uiOutput("a_overlay_gnomad_ui")),
column(4, uiOutput("a_label_gnomad_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_gnomad_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
),
fluidRow(
column(12, uiOutput("info_gnomad_ui"))
)
#fluidRow(column(12, uiOutput('a_gnomad_constraints_available_ui'))),
#fluidRow(column(12, tableOutput("a_table_gnomad_constraints_ui")))
),
box(
title = "GTEx / HPA", width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = TRUE,
fluidRow(
column(12, uiOutput('a_tissue_select_ui'),
uiOutput("a_gtex_rna_tissue_ui"),
uiOutput("a_gtex_protein_tissue_ui"),
uiOutput("a_hpa_rna_tissue_ui")),
),
fluidRow(
column(4, uiOutput("a_overlay_tissue_ui")),
column(4, uiOutput("a_label_tissue_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_tissue_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
),
fluidRow(
column(12, uiOutput("info_tissue_ui"))
)
),
box(
title ='Upload SNPs', width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = TRUE,
fluidRow(
column(12, uiOutput("a_SNP_file"))
),
fluidRow(
column(4, uiOutput("a_overlay_snp_ui")),
column(4, uiOutput("a_label_snp_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_snp_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
)
),
box(
title = "Upload genes", width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = TRUE,
fluidRow(
column(12, uiOutput("a_genes_file")),
),
fluidRow(
column(4, uiOutput("a_overlay_genes_upload_ui")),
column(4, uiOutput("a_label_genes_upload_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_gene_upload_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
)
),
box(
title = "Settings", width = NULL, solidHeader = TRUE, collapsible = TRUE, collapsed = FALSE,
fluidRow(
column(3, align = 'left', h5(strong('Overlay'))),
column(3, align = 'center', h5(strong(uiOutput("a_sig_text_ui")))),
column(3, align = 'center', h5(strong(uiOutput("a_insig_text_ui")))),
column(3, align = 'center', h5(strong('Symbol'))),
),
#fluidRow(column(12, h5('InWeb'))),
fluidRow(
column(3, h5('InWeb / iRefIndex / BioPlex')),
column(3, uiOutput("a_color_inweb_sig_ui")),
column(3, uiOutput("a_color_inweb_insig_ui")),
column(3, uiOutput("a_symbol_inweb_ui"))
),
#fluidRow(column(12, h5('GWAS catalogue'))),
fluidRow(
column(3, h5('GWAS catalog')),
column(3, uiOutput("a_color_gwas_cat_sig_ui")),
column(3, uiOutput("a_color_gwas_cat_insig_ui")),
column(3, uiOutput("a_symbol_gwas_cat_ui"))
),
#fluidRow(column(12, h5('gnomAD'))),
fluidRow(
column(3, h5('gnomAD')),
column(3, uiOutput("a_color_gnomad_sig_ui")),
column(3, uiOutput("a_color_gnomad_insig_ui")),
column(3, uiOutput("a_symbol_gnomad_ui"))
),
fluidRow(
column(3, h5('GTEx / HPA')),
column(3, uiOutput("a_color_tissue_sig_ui")),
column(3, uiOutput("a_color_tissue_insig_ui")),
column(3, uiOutput("a_symbol_tissue_ui"))
),
#fluidRow(column(12, h5('SNPs upload'))),
fluidRow(
column(3, h5('SNPs upload')),
column(3, uiOutput("a_color_snp_sig_ui")),
column(3, uiOutput("a_color_snp_insig_ui")),
column(3, uiOutput("a_symbol_snp_ui"))
),
#fluidRow(column(12, h5('genes upload'))),
fluidRow(
column(3, h5('Genes upload')),
column(3, uiOutput("a_color_genes_upload_sig_ui")),
column(3, uiOutput("a_color_genes_upload_insig_ui")),
column(3, uiOutput("a_symbol_genes_upload_ui"))
)
)
),
column(width = 8,
box(
title = tagList(shiny::icon('chart-area'), "Volcano plot"), solidHeader = TRUE, status = 'success', collapsible = TRUE, width = 12,
# height = '800px'
fluidRow(
column(12, shinyjs::hidden(myDownloadButton("a_integrated_plot_download",'Volcano plot')))
),
fluidRow(style = "padding-bottom:150px",
column(12, shinycssloaders::withSpinner(plotlyOutput("Multi_VolcanoPlot"), spinner_type)),
)
),
tabBox(
title = tagList(img(src='icon_venn_a.png',width='22px'), 'Venn diagrams'), width = 12, #status = 'success', collapsible = TRUE,
tabPanel('InWeb / iRefIndex / BioPlex',
fluidRow(
column(4, plotOutput('a_inweb_venn_ui', width = "220px", height = "220px")),
column(5, br(), br(), br(), br(), uiOutput("a_ppi_venn_verbatim_ui")),
column(3, shinyjs::hidden(myDownloadButton("a_inweb_venn_mapping_download", 'Genes', icon("download"))))
),
),
tabPanel('GWAS catalog',
fluidRow(
column(4, plotOutput('a_gwas_catalogue_venn_all_ui', width = "220px", height = "220px")),
column(5, br(), br(), br(), br(), uiOutput('a_gwas_catalogue_venn_verbatim_ui')),
column(3, shinyjs::hidden(myDownloadButton("a_gwas_catalogue_venn_mapping_download", 'Genes', icon("download"))))
),
),
tabPanel('gnomAD',
fluidRow(
column(4, plotOutput('a_gnomad_venn_ui', width = "220px", height = "220px")),
column(5, br(), br(), br(), br(), uiOutput("a_gnomad_venn_verbatim_ui")),
column(3, shinyjs::hidden(myDownloadButton("a_gnomad_venn_mapping_download", 'Genes', icon("download"))))
)
),
tabPanel('GTEx / HPA',
fluidRow(
column(4, plotOutput('a_tissue_venn_ui', width = "220px", height = "220px")),
column(5, br(), br(), br(), br(), uiOutput("a_tissue_venn_verbatim_ui")),
column(3, shinyjs::hidden(myDownloadButton("a_tissue_venn_mapping_download", 'Genes', icon("download"))))
),
),
tabPanel('SNPs upload',
fluidRow(
column(4, plotOutput('a_snp_venn_ui', width = "220px", height = "220px")),
column(5, br(), br(), br(), br(),
uiOutput('a_snp_venn_verbatim_ui')),
column(3, uiOutput('a_select_venn_snp_ui'),
uiOutput('a_select_venn_snp_loci_ui'),
shinyjs::hidden(myDownloadButton("a_snp_venn_mapping_download", 'Genes', icon("download"))))
)
),
tabPanel('Genes upload',
fluidRow(
column(4, plotOutput('a_genes_upload_venn_ui', width = "220px", height = "220px")),
column(5, br(), br(), br(), br(),
uiOutput('a_genes_upload_venn_verbatim_ui')),
column(3, uiOutput('a_select_venn_genes_upload_ui'),
shinyjs::hidden(myDownloadButton("a_genes_upload_venn_mapping_download", 'Genes', icon("download")))),
),
)
)
)
),
tabPanel("Gene set annotations", value = "p4",
br(),
column(4,
box(
title = tagList("Settings"), width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE,
fluidRow(
column(12, uiOutput("a_pf_loc_selection")),
),
fluidRow(
column(12, uiOutput("a_pathway_mapping_freq_slider_ui"))
),
fluidRow(
column(12, uiOutput("a_pathway_mapping_search_ui"))
),
fluidRow(
column(12, uiOutput("a_pathway_mapping_type_sort_ui"))
),
fluidRow(
column(8,''),
column(4, shinyjs::hidden(myDownloadButton("a_pathway_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
),
fluidRow(
column(12, uiOutput("info_geneset_ui"))
)
)
),
column(8,
box(
title = tagList(shiny::icon('chart-area'), "Volcano plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
fluidRow(
column(3, shinyjs::hidden(myDownloadButton("a_pathway_plot_download", 'Volcano plot'))),
column(3, shinyjs::hidden(myDownloadButton("a_pathway_plot_legend_download", 'Volcano plot (legend)'))),
column(6, '')
),
fluidRow(style = "padding-bottom:125px",
column(12, shinycssloaders::withSpinner(plotlyOutput('VolcanoPlotPathway'), spinner_type))
)
),
box(
title = tagList("Annotation table"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
fluidRow(
column(12, DT::dataTableOutput('a_pathway_data_table_ui'))
)
)
)
),
tabPanel("Tissue enrichment", value = "p4",
br(),
column(4,
box(
title = tagList('Settings'), width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE,
fluidRow(
column(12,
uiOutput('a_tissue_select_source_ui'),
uiOutput('a_tissue_enrichment_upload_ui'),
uiOutput('a_tissue_enrichment_type_select_ui'),
uiOutput('a_tissue_enrichment_slider_ui'),
uiOutput('a_tissue_enrichment_xaxis_ui'),
uiOutput('a_tissue_enrichment_scientific_notation_ui')
)
),
fluidRow(
column(6, uiOutput("a_button_plot_tissue_enrichment_ui")),
column(6, shinyjs::hidden(myDownloadButton("a_tissue_enrichment_download",'Tissue enrichment', img=icon('file-alt', lib = "font-awesome"))))
),
fluidRow(
column(12, uiOutput("info_tissue_enrichment_ui"))
)
)
),
column(8,
box(
title = tagList('Enrichment bar plot'), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE, height = 1000,
fluidRow(
column(12,
shinycssloaders::withSpinner(plotlyOutput('a_tissue_enrichment_ui'), spinner_type)
)
)
)
)
),
tabPanel("Inspect uploaded data (dev)", value = "p5",
fluidRow(
column(12,
DT::dataTableOutput('a_file_display_table_ui')
)
)
)
)
),
tabItem(tabName = "widgets",
shinyjs::useShinyjs(),
tabsetPanel(id = "comparison",
tabPanel("Basic plotting",
br(),
column(4,
box(
title = 'Settings for file 1', width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE,
column(12,
fluidRow(
column(6,
uiOutput("b_file_1_significance_type_ui"),
uiOutput("b_file_1_FDR_thresh"),
uiOutput("b_file_1_PVal_thresh")
),
column(6,
uiOutput('b_file_1_logfc_direction_ui'),
uiOutput("b_file_1_logFC_thresh")
)
),
fluidRow(
uiOutput('b_file_1_select_scatterplot_ui')
)
)
),
box(
title = 'Summary for file 1', width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE, collapsed = TRUE,
column(12,
fluidRow(
column(12,
uiOutput("b_file_1_summary_text_ui")
),
column(12,
tableOutput('b_file_1_summary_table_ui')
),
column(12,
shinyjs::hidden(myDownloadButton("b_file_1_mapping_download", 'Proteomic data', icon("download"))))
)
)
),
box(
title = tagList(shiny::icon('chart-area'), "Volcano plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
column(12,
fluidRow(
column(12, shinyjs::hidden(myDownloadButton("b_file_1_volcano_download", 'Volcano plot')))
),
fluidRow(
shinycssloaders::withSpinner(plotlyOutput('b_file_1_volcano'), spinner_type),
)
)
),
box(
title = tagList(img(src='icon_scatter.png',width='22px'), "Scatter plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE, collapsed = TRUE,
column(12,
fluidRow(
column(12, shinyjs::hidden(myDownloadButton("b_file_1_scatter_download", 'Scatter plot')))
),
fluidRow(
shinycssloaders::withSpinner(plotlyOutput('b_file_1_scatter'), spinner_type),
)
)
)
),
column(4,
box(
title = 'Settings for file 2', width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE,
column(12,
fluidRow(
column(6,
uiOutput("b_file_2_significance_type_ui"),
uiOutput("b_file_2_FDR_thresh"),
uiOutput("b_file_2_PVal_thresh")
),
column(6,
uiOutput('b_file_2_logfc_direction_ui'),
uiOutput("b_file_2_logFC_thresh")
)
),
fluidRow(
uiOutput('b_file_2_select_scatterplot_ui')
)
)
),
box(
title = 'Summary for file 2', width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE, collapsed = TRUE,
column(12,
fluidRow(
column(12,
uiOutput("b_file_2_summary_text_ui")
),
column(12,
tableOutput('b_file_2_summary_table_ui')
),
column(12,
shinyjs::hidden(myDownloadButton("b_file_2_mapping_download", 'Proteomic data', icon("download")))
)
)
)
),
box(
title = tagList(shiny::icon('chart-area'), "Volcano plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
column(12,
fluidRow(
column(12, shinyjs::hidden(myDownloadButton("b_file_2_volcano_download", 'Volcano plot')))
),
fluidRow(
shinycssloaders::withSpinner(plotlyOutput('b_file_2_volcano'), spinner_type),
)
)
),
box(
title = tagList(img(src='icon_scatter.png',width='22px'), "Scatter plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE, collapsed = TRUE,
column(12,
fluidRow(
column(12, shinyjs::hidden(myDownloadButton("b_file_2_scatter_download", 'Scatter plot')))
),
fluidRow(
shinycssloaders::withSpinner(plotlyOutput('b_file_2_scatter'), spinner_type),
)
)
)
),
column(4,
box(
title = 'Settings for file 3', width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE,
column(12,
fluidRow(
column(6,
uiOutput("b_file_3_significance_type_ui"),
uiOutput("b_file_3_FDR_thresh"),
uiOutput("b_file_3_PVal_thresh")
),
column(6,
uiOutput('b_file_3_logfc_direction_ui'),
uiOutput("b_file_3_logFC_thresh")
)
),
fluidRow(
uiOutput('b_file_3_select_scatterplot_ui')
)
)
),
box(
title = 'Summary for file 3', width = 12, solidHeader = TRUE, status = 'primary', collapsible = TRUE, collapsed = TRUE,
column(12,
fluidRow(
column(12,
uiOutput("b_file_3_summary_text_ui")
),
column(12,
tableOutput('b_file_3_summary_table_ui')
),
column(12,
shinyjs::hidden(myDownloadButton("b_file_3_mapping_download", 'Proteomic data', icon("download")))
)
)
)
),
box(
title = tagList(shiny::icon('chart-area'), "Volcano plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
column(12,
fluidRow(
column(12, shinyjs::hidden(myDownloadButton("b_file_3_volcano_download", 'Volcano plot')))
),
fluidRow(
shinycssloaders::withSpinner(plotlyOutput('b_file_3_volcano'), spinner_type),
)
)
),
box(
title = tagList(img(src='icon_scatter.png',width='22px'), "Scatter plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE, collapsed = TRUE,
column(12,
fluidRow(
column(12, shinyjs::hidden(myDownloadButton("b_file_3_scatter_download", 'Scatter plot')))
),
fluidRow(
shinycssloaders::withSpinner(plotlyOutput('b_file_3_scatter'), spinner_type),
)
)
)
)
),
tabPanel("Venn diagrams",
br(),
column(6,
box(
title = tagList(img(src='icon_venn_a.png',width='22px'), 'Venn diagrams'), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE, collapsed = TRUE,
column(1, ''),
column(8,
fluidRow(
plotOutput('b_file_comparison_venn_ui', width = "280px", height = "280px")
),
fluidRow(
uiOutput('b_file_comparison_venn_verbatim_ui')
)
),
column(3, '')
),
box(
title = 'Venn diagram explanations', width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
column(12,
fluidRow(
uiOutput('b_file_comparison_venn_explanations_ui')
)
)
)
),
column(6,
box(
title = 'Explore overlap', width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE, collapsed = TRUE,
fluidRow(
column(4,
uiOutput('b_file_comparison_data_table_select_ui')
),
column(4,
myDownloadButton("b_file_comparison_data_table_download_ui", 'Genes', icon("download"))
),
column(4,
''
)
),
fluidRow(
column(12,
DT::dataTableOutput('b_file_comparison_data_table_ui')
)
)
)
)
)
)
),
tabItem(tabName = "guide",
# works in browser format
tags$iframe(src = "welcome_guide_v1.0_210514.pdf",
style="width:100%;", #frameborder="0"
height = "3100px")
),
tabItem(tabName = "start",
fluidRow(
column(3, ''),
column(6,
# top of table
fluidRow(style = "padding-top:200px",
column(12, align = 'center',
h1(strong("Genoppi"), style = "font-size:100px;"),
br(),
uiOutput('a_example_file_ui'),
uiOutput('a_get_example_file_ui')
)
),
fluidRow(
br(),
h5(HTML(paste('<b>Genoppi</b> is an open-source software for performing quality control and
analyzing quantitative proteomic data. Genoppi streamlines the integration of
proteomic data with external datasets such as known protein-protein interactions
in published literature, data from genetic studies, gene set annotations, or other
user-defined inputs. See the', actionLink('tab_welcome','welcome guide'),
'for more details.') ))
),
fluidRow(style = "padding-top:300px",
column(12, align = 'center',
h6(HTML(paste0(actionLink('enable_dev_mode', 'Developer mode'))))
)
),
),
column(3, '')
)
),
tabItem(tabName = "documentation",
fluidRow(
column(1, ''),
column(10,
# top of table
fluidRow(style = "padding-top:100px",
column(12, align = 'left',
h1(strong("Data documentation"), style = "font-size:30px;"),
br(),
uiOutput('documentation_ui')
)
)
),
column(1, '')
)
)
)
)
)
sidebar <- dashboardSidebar(
sidebarMenu(id = "sidebarmenu",
#h6(as.character(genoppi.ver)),
menuItem("Quick Start", tabName = "start", icon = icon("stream")),
menuItem("Guide", tabName = "guide", icon = icon("info-circle")),
menuItem("Data Documentation", icon = icon("question-circle"), tabName = "documentation", badgeLabel = "new", badgeColor = "green"),
menuItem("Single File", tabName = "dashboard", icon = icon("file")),
menuItem("Multi Files Comparison", icon = icon("copy"), tabName = "widgets"),
conditionalPanel("input.sidebarmenu === 'dashboard'",
uiOutput("a_file"),
uiOutput("a_in_pulldown_check_ui"),
#uiOutput('a_make_example_file'),
HTML('<hr style="border-color: #D6DBE0;">'),
uiOutput("a_bait_search"),
uiOutput("a_GOI_search"),
uiOutput("a_GOI_search_alpha"),
#uiOutput("a_color_scheme"),
uiOutput("a_color_style"),
uiOutput("a_file_color"),
uiOutput("a_significance_type_ui"),
uiOutput("FDR_thresh"),
uiOutput("PVal_thresh"),
uiOutput('a_logfc_direction_ui'),
uiOutput("logFC_thresh")
),
conditionalPanel("input.sidebarmenu == 'widgets'",
uiOutput("b_file_1_ui"),
uiOutput("b_file_2_ui"),
uiOutput("b_file_3_ui"),
HTML('<hr style="border-color: #D6DBE0;">'),
uiOutput("b_GOI_search"),
uiOutput("b_GOI_search_alpha")
),
br(),
tags$footer(
tags$p(paste('version',genoppi.ver), style = "color: grey; text-align: center;")
)
)
)
# Put them together into a dashboardPage
dashboardPage(skin = "black",
#header,
dashboardHeader(title = 'Genoppi'),
sidebar,
body
)
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