inst/shiny-examples/myapp/ui.R
In frhl/genoppi-v4: 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", 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, tagList(h5(HTML(bold('Replicate corrlation(s):'))))),
),
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", 'Pulldown data', icon("download"))))
)
),
shinyjs::hidden(box(
id='box_mapping_warning_ui', title = "Gene mapping", width = NULL, solidHeader = TRUE, status = "warning", collapsible = TRUE, collapsed = FALSE,
fluidRow(
h6('Explore mapping of accession to gene symbol')
)
))
),
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, plotlyOutput("VolcanoPlot")) #, 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(
column(11, plotlyOutput("ScatterPlot")) #, width = "550px", height = "550px"
)
)
)
),
tabPanel("Integrated plotting", value = "p2",
br(),
column(width = 4,
box(
title = tagList(img(src='icon_inweb.png',width='20px'), "InWeb InBiomap"), width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = FALSE,
fluidRow(
column(12, uiOutput("a_bait_layer"))
),
fluidRow(
column(8, uiOutput("a_label_inweb_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_inweb_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
),
),
box(
title = tagList(shiny::icon('list-alt'), "GWAS catalog"), width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = TRUE,
fluidRow(
column(12, uiOutput('a_gwas_catalogue_ui'))
),
fluidRow(
column(8, uiOutput("a_label_gwas_cat_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_gwas_catalogue_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
),
),
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(8,
uiOutput('a_slide_gnomad_pli_threshold_ui'),
uiOutput('a_gnomad_colorscale_text_ui'),
#plotOutput('a_gnomad_colorscale_ui', width = "275px", height = '100px')
)
),
fluidRow(
column(8, 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('a_gnomad_constraints_available_ui'))),
#fluidRow(column(12, tableOutput("a_table_gnomad_constraints_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(12, h5('InWeb'))),
fluidRow(
column(4, uiOutput("a_color_inweb_sig_ui")),
column(4, uiOutput("a_color_inweb_insig_ui")),
column(4, uiOutput("a_symbol_inweb_ui"))
),
fluidRow(column(12, h5('GWAS catalogue'))),
fluidRow(
column(4, uiOutput("a_color_gwas_cat_sig_ui")),
column(4, uiOutput("a_color_gwas_cat_insig_ui")),
column(4, uiOutput("a_symbol_gwas_cat_ui"))
),
fluidRow(column(12, h5('gnomAD'))),
fluidRow(
column(4, uiOutput("a_color_gnomad_sig_ui")),
column(4, uiOutput("a_color_gnomad_insig_ui")),
column(4, uiOutput("a_symbol_gnomad_ui"))
),
fluidRow(column(12, h5('SNPs upload'))),
fluidRow(
column(4, uiOutput("a_color_snp_sig_ui")),
column(4, uiOutput("a_color_snp_insig_ui")),
column(4, uiOutput("a_symbol_snp_ui"))
),
fluidRow(column(12, h5('genes upload'))),
fluidRow(
column(4, uiOutput("a_color_genes_upload_sig_ui")),
column(4, uiOutput("a_color_genes_upload_insig_ui")),
column(4, 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(1, br(), br(), br(), br(), plotOutput("FDR_colorbar_integrated", width = "50px")),
column(12, plotlyOutput("Multi_VolcanoPlot")),
)
),
tabBox(
title = tagList(img(src='icon_venn_a.png',width='22px'), 'Venn diagrams'), width = 12, #status = 'success', collapsible = TRUE,
tabPanel('InWeb',
fluidRow(
column(4, plotOutput('a_inweb_venn_ui', width = "220px", height = "220px")),
column(5, br(), br(), br(), br(), uiOutput("a_inweb_venn_verbatim_ui")),
column(3, shinyjs::hidden(myDownloadButton("a_inweb_venn_mapping_download", 'overlap', 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", 'overlap', 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", 'overlap', 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", 'overlap', 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", 'overlap', 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")),
#column(5, uiOutput("a_PF_sort_col")),
#column(5, uiOutput("a_BPF_freq"))
),
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"))))
)
)
),
column(8,
box(
title = tagList("Volcano plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
fluidRow(
column(11, shinyjs::hidden(myDownloadButton("a_pathway_plot_download", 'Gene sets plot')))
),
fluidRow(style = "padding-bottom:125px",
column(12, plotlyOutput('VolcanoPlotPathway'))
)
),
box(
title = tagList("Annotation table"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
fluidRow(
column(12, DT::dataTableOutput('a_pathway_data_table_ui'))
)
)
)
)
)
),
tabItem(tabName = "widgets",
shinyjs::useShinyjs(),
tabsetPanel(id = "comparison",
tabPanel("Basic Plots", value = "3_p1",
br(),
fluidRow(
column(3, uiOutput("c_prot_fam_db")),
column(2, uiOutput("c_text_prot_fam_db")),
column(3, uiOutput("c_color_theme_pf"))
),
fluidRow(
column(4, downloadButton("download_c1_pf_cleaned_input", "Remove selected PF from f1")),
column(4, downloadButton("download_c2_pf_cleaned_input", "Remove selected PF from f2")),
column(4, downloadButton("download_c3_pf_cleaned_input", "Remove selected PF from f3"))
),
fluidRow(
column(4, uiOutput("c_color_setting_text"))
),
fluidRow(
column(4, uiOutput("c_color_theme"))
),
fluidRow(
column(4, uiOutput("c_color_theme_indv_sig")),
column(4, uiOutput("c_color_theme_indv_insig"))
),
br(),
fluidRow(
column(3, plotOutput("c_FDR_colorbar", height = "100px"))
),
fluidRow(
column(1, myDownloadButton("download_c_vp1_gg", "Volcano")),
column(3),
column(1, myDownloadButton("download_c_vp2_gg", "Volcano")),
column(3),
column(1, myDownloadButton("download_c_vp3_gg", "Volcano"))
),
fluidRow(
column(4, plotlyOutput("VolcanoPlot_c1")),
column(4, plotlyOutput("VolcanoPlot_c2")),
column(4, plotlyOutput("VolcanoPlot_c3"))
),
br(),
fluidRow(
column(1, myDownloadButton("download_c_sp1_gg", "Scatter")),
column(3),
column(1, myDownloadButton("download_c_sp2_gg", "Scatter")),
column(3),
column(1, myDownloadButton("download_c_sp3_gg", "Scatter"))
),
fluidRow(
column(4, plotlyOutput("ScatterPlot_c1")),
column(4, plotlyOutput("ScatterPlot_c2")),
column(4, plotlyOutput("ScatterPlot_c3"))
)
),
tabPanel("Protein Comparison", value = "3_p2",
br(),
fluidRow(
column(8, uiOutput("c_comparison_text")),
column(4, uiOutput("c_pc_plot_button"))
),
br(),
fluidRow(
column(4, uiOutput("c_comparison_text_f1")),
column(4, uiOutput("c_comparison_text_f2")),
column(4, uiOutput("c_comparison_text_f3"))
),
br(),
fluidRow(
column(4, uiOutput("c_comparison1_FDR_slider")),
column(4, uiOutput("c_comparison2_FDR_slider")),
column(4, uiOutput("c_comparison3_FDR_slider"))
),
fluidRow(
column(4, uiOutput("c_comparison1_pvalue_slider")),
column(4, uiOutput("c_comparison2_pvalue_slider")),
column(4, uiOutput("c_comparison3_pvalue_slider"))
),
fluidRow(
column(4, uiOutput("c_comparison_logFC_slider1")),
column(4, uiOutput("c_comparison_logFC_slider2")),
column(4, uiOutput("c_comparison_logFC_slider3"))
),
br(),
fluidRow(
column(4, plotlyOutput("comparison1")),
column(4, plotlyOutput("comparison2")),
column(4, plotlyOutput("comparison3")) #, width = "370px", height = "300px")
),
br(),
fluidRow(
column(4, plotlyOutput("comparison1_scatter")),
column(4, plotlyOutput("comparison2_scatter")),
column(4, plotlyOutput("comparison3_scatter")) #, width = "370px", height = "300px")
),
fluidRow(
column(4, uiOutput("c_VennDiagram_legend"))
),
br(),
fluidRow(
column(4, plotOutput("c_VennDiagram", width = "220px", height = "220px")),
column(8, tableOutput("c_unique"))
)
),
tabPanel("InWeb", value = "3_p3",
br(),
fluidRow(
column(4, uiOutput("c_bait_layer")),
column(2, uiOutput("c_text_inweb")),
column(2, uiOutput("c_button_inweb"))
),
fluidRow(
column(4, uiOutput("c_color_setting_text_inweb"))
),
fluidRow(
column(2, uiOutput("c_color_theme_inweb_sig")),
column(2, uiOutput("c_color_theme_inweb_insig")),
column(2, uiOutput("c_color_theme_tab3")),
column(2, uiOutput("c_marker_theme_inweb"))
),
br(),
fluidRow(
column(3, plotOutput("c_inweb_colorbar", height = "100px"))
),
br(),
fluidRow(
column(1, myDownloadButton("download_c_vp1_inweb_gg", "Volcano")),
column(3),
column(1, myDownloadButton("download_c_vp2_inweb_gg", "Volcano")),
column(3),
column(1, myDownloadButton("download_c_vp3_inweb_gg", "Volcano"))
),
fluidRow(
column(4, plotlyOutput("VolcanoPlot_c1_inweb")),
column(4, plotlyOutput("VolcanoPlot_c2_inweb")),
column(4, plotlyOutput("VolcanoPlot_c3_inweb"))
),
br(),
br(),
fluidRow(
column(4, plotOutput("c_VennDiagram_inweb", width = "220px", height = "220px")),
column(8, tableOutput("c_unique_inweb"))
)
),
tabPanel("GOI", value = "3_p4",
br(),
fluidRow(
column(4, uiOutput("c_genes_file")),
column(2, uiOutput("c_text_goi")),
column(2, uiOutput("c_button_goi"))
),
fluidRow(
column(4, uiOutput("c_color_setting_text_goi"))
),
fluidRow(
column(2, uiOutput("c_color_theme_goi_sig")),
column(2, uiOutput("c_color_theme_goi_insig")),
column(2, uiOutput("c_color_theme_tab4")),
column(2, uiOutput("c_marker_theme_goi"))
),
br(),
fluidRow(
column(3, plotOutput("c_goi_colorbar", height = "100px"))
),
br(),
fluidRow(
column(1, myDownloadButton("download_c_vp1_goi_gg", "Volcano")),
column(3),
column(1, myDownloadButton("download_c_vp2_goi_gg", "Volcano")),
column(3),
column(1, myDownloadButton("download_c_vp3_goi_gg", "Volcano"))
),
fluidRow(
column(4, plotlyOutput("VolcanoPlot_c1_goi")),
column(4, plotlyOutput("VolcanoPlot_c2_goi")),
column(4, plotlyOutput("VolcanoPlot_c3_goi"))
),
br(),
fluidRow(
column(4, uiOutput("c_goi_num_inputs"))
),
br(),
br(),
fluidRow(
column(4, plotOutput("c_VennDiagram_goi", width = "220px", height = "220px")),
column(8, tableOutput("c_unique_goi"))
)
),
tabPanel("Protein Family", value = "3_p6",
br(),
fluidRow(
column(4, uiOutput("c_pf_FDR_slider1")),
column(4, uiOutput("c_pf_FDR_slider2")),
column(4, uiOutput("c_pf_FDR_slider3"))
),
fluidRow(
column(4, uiOutput("c_pf_pvalue_slider1")),
column(4, uiOutput("c_pf_pvalue_slider2")),
column(4, uiOutput("c_pf_pvalue_slider3"))
),
fluidRow(
column(4, uiOutput("c_pf_logFC_slider1")),
column(4, uiOutput("c_pf_logFC_slider2")),
column(4, uiOutput("c_pf_logFC_slider3"))
),
fluidRow(
column(3, uiOutput("c_PF_marker_size")),
column(3, uiOutput("c_PF_sort_col")),
column(3, uiOutput("c_PF_freq")),
column(3, uiOutput("c_PF_button"))
),
fluidRow(
column(3, uiOutput("c_pf_loc_selection"))
),
br(),
fluidRow(
column(12, plotlyOutput("comparison1_pf"))
),
fluidRow(
column(12, plotlyOutput("comparison2_pf"))
),
fluidRow(
column(12, plotlyOutput("comparison3_pf"))
)
),
tabPanel("PFE", value = "q1",
br(),
fluidRow(
column(4, uiOutput("b_PF_FDR_slider")),
column(4, uiOutput("b_PF_logFC_slider")),
column(4, uiOutput("b_PF_pvalue_slider"))
),
fluidRow(
column(3, uiOutput("b_PF_marker_size")),
column(3, uiOutput("b_PF_sort_col")),
column(3, uiOutput("b_PF_freq"))
),
fluidRow(column(3, uiOutput("b_pf_loc_selection")),
column(3, uiOutput("b_PF_button"))
),
fluidRow(
column(12, plotlyOutput("Protein_Family"), height = "800px")
)
),
tabPanel("Download", value = "3_p7",
br(),
fluidRow(
column(3, downloadButton("c1_download_mapped_uniprot", "Converted identifiers f1")),
column(3, downloadButton("c2_download_mapped_uniprot", "Converted identifiers f2")),
column(3, downloadButton("c3_download_mapped_uniprot", "Converted identifiers f3"))
),
br(),
fluidRow(
column(3, downloadButton("c1_download_replications_calculated", "Calculated mod ttest f1")),
column(3, downloadButton("c2_download_replications_calculated", "Calculated mod ttest f2")),
column(3, downloadButton("c3_download_replications_calculated", "Calculated mod ttest f3"))
),
# br(),
# fluidRow(
# column(2, downloadButton("c_download_snp_to_genes", "SNP to gene"))
# ),
hr(),
fluidRow(
column(3, downloadButton("c_download_basic_plots", "Basic Plots"))
),
br(),
fluidRow(
column(3, downloadButton("c_download_protein_comparisons", "Protein comparisons"))
),
br(),
fluidRow(
column(3, downloadButton("c_download_inweb", "InWeb comparisons"))
),
br(),
fluidRow(
column(3, downloadButton("c_download_goi", "GOI comparisons"))
),
# br(),
# fluidRow(
# column(3, downloadButton("c_download_snp", "SNP comparisons"))
# ),
br(),
fluidRow(
column(3, downloadButton("c_download_protein_fams", "Protein families"))
)
)
)
),
tabItem(tabName = "guide",
# works in browser format
tags$iframe(src = "welcome_guide_200415.pdf",
style="width:100%;", #frameborder="0"
height = "3100px")
)
)
)
)
sidebar <- dashboardSidebar(
sidebarMenu(id = "sidebarmenu",
menuItem("Welcome Guide", tabName = "guide", icon = icon("info-circle")),
menuItem("Single File", tabName = "dashboard", icon = icon("file")),
menuItem("Multi Files Comparison", icon = icon("copy"), tabName = "widgets"),
conditionalPanel("input.sidebarmenu === 'dashboard'",
uiOutput("a_file"),
HTML('<hr style="border-color: #D6DBE0;">'),
uiOutput("a_bait_search"),
uiOutput("a_GOI_search"),
#uiOutput("a_color_scheme"),
uiOutput("a_color_style"),
uiOutput("a_file_color"),
uiOutput("a_significance_type_ui"),
uiOutput("FDR_thresh"),
uiOutput("PVal_thresh"),
uiOutput('a_logfc_direction_ui'),
uiOutput("logFC_thresh")
),
conditionalPanel("input.sidebarmenu === 'widgets'",
uiOutput("c_file1"),
uiOutput("c_file2"),
uiOutput("c_file3"),
HTML('<hr style="border-color: #D6DBE0;">'),
uiOutput("c_GOI_search"),
uiOutput("c_color_scheme"),
uiOutput("c_color_style"),
uiOutput("c_file_color"),
uiOutput("c_FDR_thresh"),
uiOutput("c_PVal_thresh"),
uiOutput("c_logFC_thresh_combined")
)
)
)
# Put them together into a dashboardPage
dashboardPage(skin = "black",
dashboardHeader(title = "Genoppi"),
sidebar,
body
)
frhl/genoppi-v4 documentation built on May 5, 2020, 7:16 a.m.
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body <- dashboardBody(
tags$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", 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, tagList(h5(HTML(bold('Replicate corrlation(s):'))))),
),
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", 'Pulldown data', icon("download"))))
)
),
shinyjs::hidden(box(
id='box_mapping_warning_ui', title = "Gene mapping", width = NULL, solidHeader = TRUE, status = "warning", collapsible = TRUE, collapsed = FALSE,
fluidRow(
h6('Explore mapping of accession to gene symbol')
)
))
),
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, plotlyOutput("VolcanoPlot")) #, 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(
column(11, plotlyOutput("ScatterPlot")) #, width = "550px", height = "550px"
)
)
)
),
tabPanel("Integrated plotting", value = "p2",
br(),
column(width = 4,
box(
title = tagList(img(src='icon_inweb.png',width='20px'), "InWeb InBiomap"), width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = FALSE,
fluidRow(
column(12, uiOutput("a_bait_layer"))
),
fluidRow(
column(8, uiOutput("a_label_inweb_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_inweb_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
),
),
box(
title = tagList(shiny::icon('list-alt'), "GWAS catalog"), width = NULL, solidHeader = TRUE, status = "primary", collapsible = TRUE, collapsed = TRUE,
fluidRow(
column(12, uiOutput('a_gwas_catalogue_ui'))
),
fluidRow(
column(8, uiOutput("a_label_gwas_cat_ui")),
column(4, shinyjs::hidden(myDownloadButton("a_gwas_catalogue_mapping_download",'Mapping', img=icon('file-alt', lib = "font-awesome"))))
),
),
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(8,
uiOutput('a_slide_gnomad_pli_threshold_ui'),
uiOutput('a_gnomad_colorscale_text_ui'),
#plotOutput('a_gnomad_colorscale_ui', width = "275px", height = '100px')
)
),
fluidRow(
column(8, 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('a_gnomad_constraints_available_ui'))),
#fluidRow(column(12, tableOutput("a_table_gnomad_constraints_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(12, h5('InWeb'))),
fluidRow(
column(4, uiOutput("a_color_inweb_sig_ui")),
column(4, uiOutput("a_color_inweb_insig_ui")),
column(4, uiOutput("a_symbol_inweb_ui"))
),
fluidRow(column(12, h5('GWAS catalogue'))),
fluidRow(
column(4, uiOutput("a_color_gwas_cat_sig_ui")),
column(4, uiOutput("a_color_gwas_cat_insig_ui")),
column(4, uiOutput("a_symbol_gwas_cat_ui"))
),
fluidRow(column(12, h5('gnomAD'))),
fluidRow(
column(4, uiOutput("a_color_gnomad_sig_ui")),
column(4, uiOutput("a_color_gnomad_insig_ui")),
column(4, uiOutput("a_symbol_gnomad_ui"))
),
fluidRow(column(12, h5('SNPs upload'))),
fluidRow(
column(4, uiOutput("a_color_snp_sig_ui")),
column(4, uiOutput("a_color_snp_insig_ui")),
column(4, uiOutput("a_symbol_snp_ui"))
),
fluidRow(column(12, h5('genes upload'))),
fluidRow(
column(4, uiOutput("a_color_genes_upload_sig_ui")),
column(4, uiOutput("a_color_genes_upload_insig_ui")),
column(4, 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(1, br(), br(), br(), br(), plotOutput("FDR_colorbar_integrated", width = "50px")),
column(12, plotlyOutput("Multi_VolcanoPlot")),
)
),
tabBox(
title = tagList(img(src='icon_venn_a.png',width='22px'), 'Venn diagrams'), width = 12, #status = 'success', collapsible = TRUE,
tabPanel('InWeb',
fluidRow(
column(4, plotOutput('a_inweb_venn_ui', width = "220px", height = "220px")),
column(5, br(), br(), br(), br(), uiOutput("a_inweb_venn_verbatim_ui")),
column(3, shinyjs::hidden(myDownloadButton("a_inweb_venn_mapping_download", 'overlap', 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", 'overlap', 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", 'overlap', 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", 'overlap', 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", 'overlap', 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")),
#column(5, uiOutput("a_PF_sort_col")),
#column(5, uiOutput("a_BPF_freq"))
),
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"))))
)
)
),
column(8,
box(
title = tagList("Volcano plot"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
fluidRow(
column(11, shinyjs::hidden(myDownloadButton("a_pathway_plot_download", 'Gene sets plot')))
),
fluidRow(style = "padding-bottom:125px",
column(12, plotlyOutput('VolcanoPlotPathway'))
)
),
box(
title = tagList("Annotation table"), width = 12, solidHeader = TRUE, status = 'success', collapsible = TRUE,
fluidRow(
column(12, DT::dataTableOutput('a_pathway_data_table_ui'))
)
)
)
)
)
),
tabItem(tabName = "widgets",
shinyjs::useShinyjs(),
tabsetPanel(id = "comparison",
tabPanel("Basic Plots", value = "3_p1",
br(),
fluidRow(
column(3, uiOutput("c_prot_fam_db")),
column(2, uiOutput("c_text_prot_fam_db")),
column(3, uiOutput("c_color_theme_pf"))
),
fluidRow(
column(4, downloadButton("download_c1_pf_cleaned_input", "Remove selected PF from f1")),
column(4, downloadButton("download_c2_pf_cleaned_input", "Remove selected PF from f2")),
column(4, downloadButton("download_c3_pf_cleaned_input", "Remove selected PF from f3"))
),
fluidRow(
column(4, uiOutput("c_color_setting_text"))
),
fluidRow(
column(4, uiOutput("c_color_theme"))
),
fluidRow(
column(4, uiOutput("c_color_theme_indv_sig")),
column(4, uiOutput("c_color_theme_indv_insig"))
),
br(),
fluidRow(
column(3, plotOutput("c_FDR_colorbar", height = "100px"))
),
fluidRow(
column(1, myDownloadButton("download_c_vp1_gg", "Volcano")),
column(3),
column(1, myDownloadButton("download_c_vp2_gg", "Volcano")),
column(3),
column(1, myDownloadButton("download_c_vp3_gg", "Volcano"))
),
fluidRow(
column(4, plotlyOutput("VolcanoPlot_c1")),
column(4, plotlyOutput("VolcanoPlot_c2")),
column(4, plotlyOutput("VolcanoPlot_c3"))
),
br(),
fluidRow(
column(1, myDownloadButton("download_c_sp1_gg", "Scatter")),
column(3),
column(1, myDownloadButton("download_c_sp2_gg", "Scatter")),
column(3),
column(1, myDownloadButton("download_c_sp3_gg", "Scatter"))
),
fluidRow(
column(4, plotlyOutput("ScatterPlot_c1")),
column(4, plotlyOutput("ScatterPlot_c2")),
column(4, plotlyOutput("ScatterPlot_c3"))
)
),
tabPanel("Protein Comparison", value = "3_p2",
br(),
fluidRow(
column(8, uiOutput("c_comparison_text")),
column(4, uiOutput("c_pc_plot_button"))
),
br(),
fluidRow(
column(4, uiOutput("c_comparison_text_f1")),
column(4, uiOutput("c_comparison_text_f2")),
column(4, uiOutput("c_comparison_text_f3"))
),
br(),
fluidRow(
column(4, uiOutput("c_comparison1_FDR_slider")),
column(4, uiOutput("c_comparison2_FDR_slider")),
column(4, uiOutput("c_comparison3_FDR_slider"))
),
fluidRow(
column(4, uiOutput("c_comparison1_pvalue_slider")),
column(4, uiOutput("c_comparison2_pvalue_slider")),
column(4, uiOutput("c_comparison3_pvalue_slider"))
),
fluidRow(
column(4, uiOutput("c_comparison_logFC_slider1")),
column(4, uiOutput("c_comparison_logFC_slider2")),
column(4, uiOutput("c_comparison_logFC_slider3"))
),
br(),
fluidRow(
column(4, plotlyOutput("comparison1")),
column(4, plotlyOutput("comparison2")),
column(4, plotlyOutput("comparison3")) #, width = "370px", height = "300px")
),
br(),
fluidRow(
column(4, plotlyOutput("comparison1_scatter")),
column(4, plotlyOutput("comparison2_scatter")),
column(4, plotlyOutput("comparison3_scatter")) #, width = "370px", height = "300px")
),
fluidRow(
column(4, uiOutput("c_VennDiagram_legend"))
),
br(),
fluidRow(
column(4, plotOutput("c_VennDiagram", width = "220px", height = "220px")),
column(8, tableOutput("c_unique"))
)
),
tabPanel("InWeb", value = "3_p3",
br(),
fluidRow(
column(4, uiOutput("c_bait_layer")),
column(2, uiOutput("c_text_inweb")),
column(2, uiOutput("c_button_inweb"))
),
fluidRow(
column(4, uiOutput("c_color_setting_text_inweb"))
),
fluidRow(
column(2, uiOutput("c_color_theme_inweb_sig")),
column(2, uiOutput("c_color_theme_inweb_insig")),
column(2, uiOutput("c_color_theme_tab3")),
column(2, uiOutput("c_marker_theme_inweb"))
),
br(),
fluidRow(
column(3, plotOutput("c_inweb_colorbar", height = "100px"))
),
br(),
fluidRow(
column(1, myDownloadButton("download_c_vp1_inweb_gg", "Volcano")),
column(3),
column(1, myDownloadButton("download_c_vp2_inweb_gg", "Volcano")),
column(3),
column(1, myDownloadButton("download_c_vp3_inweb_gg", "Volcano"))
),
fluidRow(
column(4, plotlyOutput("VolcanoPlot_c1_inweb")),
column(4, plotlyOutput("VolcanoPlot_c2_inweb")),
column(4, plotlyOutput("VolcanoPlot_c3_inweb"))
),
br(),
br(),
fluidRow(
column(4, plotOutput("c_VennDiagram_inweb", width = "220px", height = "220px")),
column(8, tableOutput("c_unique_inweb"))
)
),
tabPanel("GOI", value = "3_p4",
br(),
fluidRow(
column(4, uiOutput("c_genes_file")),
column(2, uiOutput("c_text_goi")),
column(2, uiOutput("c_button_goi"))
),
fluidRow(
column(4, uiOutput("c_color_setting_text_goi"))
),
fluidRow(
column(2, uiOutput("c_color_theme_goi_sig")),
column(2, uiOutput("c_color_theme_goi_insig")),
column(2, uiOutput("c_color_theme_tab4")),
column(2, uiOutput("c_marker_theme_goi"))
),
br(),
fluidRow(
column(3, plotOutput("c_goi_colorbar", height = "100px"))
),
br(),
fluidRow(
column(1, myDownloadButton("download_c_vp1_goi_gg", "Volcano")),
column(3),
column(1, myDownloadButton("download_c_vp2_goi_gg", "Volcano")),
column(3),
column(1, myDownloadButton("download_c_vp3_goi_gg", "Volcano"))
),
fluidRow(
column(4, plotlyOutput("VolcanoPlot_c1_goi")),
column(4, plotlyOutput("VolcanoPlot_c2_goi")),
column(4, plotlyOutput("VolcanoPlot_c3_goi"))
),
br(),
fluidRow(
column(4, uiOutput("c_goi_num_inputs"))
),
br(),
br(),
fluidRow(
column(4, plotOutput("c_VennDiagram_goi", width = "220px", height = "220px")),
column(8, tableOutput("c_unique_goi"))
)
),
tabPanel("Protein Family", value = "3_p6",
br(),
fluidRow(
column(4, uiOutput("c_pf_FDR_slider1")),
column(4, uiOutput("c_pf_FDR_slider2")),
column(4, uiOutput("c_pf_FDR_slider3"))
),
fluidRow(
column(4, uiOutput("c_pf_pvalue_slider1")),
column(4, uiOutput("c_pf_pvalue_slider2")),
column(4, uiOutput("c_pf_pvalue_slider3"))
),
fluidRow(
column(4, uiOutput("c_pf_logFC_slider1")),
column(4, uiOutput("c_pf_logFC_slider2")),
column(4, uiOutput("c_pf_logFC_slider3"))
),
fluidRow(
column(3, uiOutput("c_PF_marker_size")),
column(3, uiOutput("c_PF_sort_col")),
column(3, uiOutput("c_PF_freq")),
column(3, uiOutput("c_PF_button"))
),
fluidRow(
column(3, uiOutput("c_pf_loc_selection"))
),
br(),
fluidRow(
column(12, plotlyOutput("comparison1_pf"))
),
fluidRow(
column(12, plotlyOutput("comparison2_pf"))
),
fluidRow(
column(12, plotlyOutput("comparison3_pf"))
)
),
tabPanel("PFE", value = "q1",
br(),
fluidRow(
column(4, uiOutput("b_PF_FDR_slider")),
column(4, uiOutput("b_PF_logFC_slider")),
column(4, uiOutput("b_PF_pvalue_slider"))
),
fluidRow(
column(3, uiOutput("b_PF_marker_size")),
column(3, uiOutput("b_PF_sort_col")),
column(3, uiOutput("b_PF_freq"))
),
fluidRow(column(3, uiOutput("b_pf_loc_selection")),
column(3, uiOutput("b_PF_button"))
),
fluidRow(
column(12, plotlyOutput("Protein_Family"), height = "800px")
)
),
tabPanel("Download", value = "3_p7",
br(),
fluidRow(
column(3, downloadButton("c1_download_mapped_uniprot", "Converted identifiers f1")),
column(3, downloadButton("c2_download_mapped_uniprot", "Converted identifiers f2")),
column(3, downloadButton("c3_download_mapped_uniprot", "Converted identifiers f3"))
),
br(),
fluidRow(
column(3, downloadButton("c1_download_replications_calculated", "Calculated mod ttest f1")),
column(3, downloadButton("c2_download_replications_calculated", "Calculated mod ttest f2")),
column(3, downloadButton("c3_download_replications_calculated", "Calculated mod ttest f3"))
),
# br(),
# fluidRow(
# column(2, downloadButton("c_download_snp_to_genes", "SNP to gene"))
# ),
hr(),
fluidRow(
column(3, downloadButton("c_download_basic_plots", "Basic Plots"))
),
br(),
fluidRow(
column(3, downloadButton("c_download_protein_comparisons", "Protein comparisons"))
),
br(),
fluidRow(
column(3, downloadButton("c_download_inweb", "InWeb comparisons"))
),
br(),
fluidRow(
column(3, downloadButton("c_download_goi", "GOI comparisons"))
),
# br(),
# fluidRow(
# column(3, downloadButton("c_download_snp", "SNP comparisons"))
# ),
br(),
fluidRow(
column(3, downloadButton("c_download_protein_fams", "Protein families"))
)
)
)
),
tabItem(tabName = "guide",
# works in browser format
tags$iframe(src = "welcome_guide_200415.pdf",
style="width:100%;", #frameborder="0"
height = "3100px")
)
)
)
)
sidebar <- dashboardSidebar(
sidebarMenu(id = "sidebarmenu",
menuItem("Welcome Guide", tabName = "guide", icon = icon("info-circle")),
menuItem("Single File", tabName = "dashboard", icon = icon("file")),
menuItem("Multi Files Comparison", icon = icon("copy"), tabName = "widgets"),
conditionalPanel("input.sidebarmenu === 'dashboard'",
uiOutput("a_file"),
HTML('<hr style="border-color: #D6DBE0;">'),
uiOutput("a_bait_search"),
uiOutput("a_GOI_search"),
#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("c_file1"),
uiOutput("c_file2"),
uiOutput("c_file3"),
HTML('<hr style="border-color: #D6DBE0;">'),
uiOutput("c_GOI_search"),
uiOutput("c_color_scheme"),
uiOutput("c_color_style"),
uiOutput("c_file_color"),
uiOutput("c_FDR_thresh"),
uiOutput("c_PVal_thresh"),
uiOutput("c_logFC_thresh_combined")
)
)
)
# Put them together into a dashboardPage
dashboardPage(skin = "black",
dashboardHeader(title = "Genoppi"),
sidebar,
body
)
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