inst/ui.R
In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App
library(shiny)
library(shinyjs)
library(dplyr)
mytheme <- fresh::create_theme(
fresh::adminlte_color(
light_blue = "#434C5E",
red = "#D81B60",
green = "#434C5E",
yellow = "#f39c12",
aqua = "#39CCCC"
),
fresh::adminlte_sidebar(
dark_bg = "#D8DEE9",
dark_hover_bg = "#81A1C1",
dark_color = "#2E3440"),
fresh::adminlte_global(
content_bg = "#FFF",
)
)
shinyUI(shinydashboardPlus::dashboardPage(freshTheme = mytheme,
header = shinydashboardPlus::dashboardHeader(
title = tagList(
span(class = "logo-lg", "ChromSCape"),
icon("ellipsis-h")),
leftUi = tagList(uiOutput("dropdown_feature_select_ui"),
br(),
br(),
uiOutput("download_scExp_UI"))
),
sidebar = shinydashboardPlus::dashboardSidebar(
shinydashboard::sidebarUserPanel(
"Vallot Lab",
subtitle = a(href = "https://github.com/vallotlab/ChromSCape/", icon("github"), "GitHub"),
image = "LogoCurie.png"
),
shinydashboard::sidebarMenu(id="tabs",
shinydashboard::menuItem("Select & Import", tabName = "select_import", icon=icon("upload")),
shinydashboard::menuItem("Filter & Normalize", tabName = "filter_normalize", icon=icon("fas fa-filter", verify_fa = FALSE)),
shinydashboard::menuItem("Visualize Cells", tabName = "vizualize_dim_red", icon=icon("fas fa-image")),
shinydashboard::menuItem("Cluster Cells", tabName = "cons_clustering", icon=icon("th")),
shinydashboard::menuItem("Coverage & Peak Calling", tabName = "coverage", icon=icon("chart-area")),
shinydashboard::menuItem("Differential Analysis", tabName = "diff_analysis", icon=icon("sort-amount-up")),
shinydashboard::menuItem("Gene Set Analysis", tabName = "enrich_analysis", icon=icon("code-branch")),
shinydashboard::menuItem("TF analysis", tabName = "TF_analysis", icon=icon("bezier-curve")),
shinydashboard::menuItem("Generate Report & Close App", tabName = "close_and_save", icon=icon("close", verify_fa = FALSE)),
shinydashboard::menuItem(
badgeColor = "green",
expandedName = "hello",
startExpanded = TRUE,
" ", column(width = 12, actionButton("popupUMAP", width = "70%", class = "btn-default",
label = "UMAP", icon = icon("fas fa-image")))
)
)
),
controlbar = shinydashboardPlus::dashboardControlbar(
id = "controlbar",
shinydashboardPlus::controlbarMenu(
id = "menu",
shinydashboardPlus::controlbarItem(
title = "Visualisation Settings",
icon = icon("chart-bar"),
h4("UMAP"), br(),
sliderInput("options.dotplot_downsampling", "Downsampled cells",
min = 500, max = 100000, step = 10, value = getOption("ChromSCape_options")$dotplot_downsample),
sliderInput("options.dotplot_size", "Point size",
min = 0.01, max = 5, step = 0.01, value = getOption("ChromSCape_options")$dotplot_size),
sliderInput("options.dotplot_transparency", "Point transparency",
min = 0.01, max = 1, step = 0.01, value = getOption("ChromSCape_options")$dotplot_transparency),
sliderInput("options.dotplot_max_distanceToTSS", "Max. distance to TSS",
min = 0, max = 100000, step = 100, value = getOption("ChromSCape_options")$dotplot_max_distanceToTSS),
sliderInput("options.dotplot_min_quantile", "Remove lower range outlier",
min = 0, max = 1, step = 0.01, value = getOption("ChromSCape_options")$dotplot_min_quantile),
sliderInput("options.dotplot_max_quantile", "Remove higher range outlier",
min = 0, max = 1, step = 0.01, value = getOption("ChromSCape_options")$dotplot_max_quantile),
h4("Heatmap"), br(),
sliderInput("options.heatmap_downsampling", "Downsampled cells",
min = 500, max = 20000, step = 10, value = getOption("ChromSCape_options")$heatmap_downsample)
),
shinydashboardPlus::controlbarItem(
title = "Parallel Settings",
icon = icon("align-left"),
selectInput("options.nb_workers","Select number of workers for parallel computation",
choices= seq_len(future::availableCores()), selected = BiocParallel::bpworkers(BiocParallel::bpparam())),
selectInput("options.bpparam_class","Select parallel computation type",
choices = names(BiocParallel::registered()), selected = 1)
)
)
),
body = shinydashboard::dashboardBody(
shinyjs::useShinyjs(),
tags$head(tags$link(rel="shortcut icon", href="ChromSCape_logo.png")),
tags$head(includeCSS('www/style.css')),
tags$head(includeCSS('www/introjs.min.css')),
tags$head(includeCSS('www/app.css')),
tags$style(type="text/css",
".shiny-output-error { visibility: hidden; }",
".shiny-output-error:before { visibility: hidden; }"
),
tags$head(tags$style(HTML(
'.myClass {
font-size: 20px;
line-height: 50px;
text-align: left;
font-family: "Helvetica Neue",Helvetica,Arial,sans-serif;
padding: 0 15px;
overflow: hidden;
color: white;
}
'))),
tags$script(HTML('
$(document).ready(function() {
$("header").find("nav").append(\'<div id="pageHeader" class="myClass"></div>\');
})
')),
shinydashboard::tabItems(
###############################################################
# 1. Select Analysis & Import dataset
###############################################################
shinydashboard::tabItem(tabName = "select_import",
fluidPage(
# Add ressources for UX
shiny::includeScript(file.path(system.file(package="ChromSCape"),"js.cookie.js")),
shiny::includeScript(file.path(system.file(package="ChromSCape"),"intro.min.js")),
shiny::includeScript(file.path(system.file(package="ChromSCape"),"app.js")),
shiny::includeScript(file.path(system.file(package="ChromSCape"),"www","shiny_js_functions.js")),
shinyWidgets::chooseSliderSkin("Flat", color = "#112446"),
#Load shinyJS added functions
shinyjs::extendShinyjs(script = file.path(system.file(package="ChromSCape"),"www","shiny_js_functions.js"),
functions = c("init_directory","save_cookie","disableTab","enableTab")),
#Center Panel
column(width=6,align="left",
shinydashboard::box(title=tagList(shiny::icon("folder"), " Select output directory"), width = NULL, status="success",
solidHeader=TRUE,
column(12, align="left",
shinyFiles::shinyDirButton("data_folder", icon = icon("folder-open"), label = "Browse", title = "Upload") %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "output_directory"), br(),
verbatimTextOutput("directory", placeholder = TRUE)),
column(12, align="left", textOutput("data_folder_info"))),
shinydashboard::box(title=tagList(shiny::icon("upload"), " Import raw data & Create new analysis"), width = NULL, status="success", solidHeader=TRUE,
column(8, br()) %>%
shinyhelper::helper(type = 'markdown', colour = "#E6C717", icon = "question-circle",
content = "HistoneMark_recommandations"),
column(12, align="left",
column(12, align="left",textInput("new_analysis_name", "Enter a name for the new analysis :", value = "Analysis_1"),
selectInput("annotation","Select reference genome:", choices=c("hg38", "mm10", "ce11")),
textOutput("data_matrices_info") %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "datamatrix_input")),
column(6,
radioButtons("data_choice_box", label = "Input data type",
choices = list("Dense Matrix"="DenseMatrix",
"Sparse Matrix" = "SparseMatrix",
"Fragment File" = "FragmentFile",
"Single-cell BAM files" = "scBAM",
"Single-cell BED files" = "scBED"
))),
column(6,
uiOutput("input_data_ui")),
column(12,
uiOutput("advanced_data_input")),
column(3, uiOutput("rebin_matrices_checkbox_ui") %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "rebin_matrices")) ,
column(12,uiOutput("rebin_matrices_ui")),
column(3, actionButton("create_analysis", "Create analysis")),
column(4, uiOutput("add_to_current_analysis_checkbox_UI"))
))
),
column(6,
column(11, align="left",
shinydashboard::box(title=tagList(shiny::icon("file"), " Current analysis"), width = NULL, status="success", solidHeader=TRUE,
column(12, align="left",
uiOutput("selected_analysis")
)),
uiOutput("rename_file_box")),
column(1, actionButton("startHelp","Help", icon = icon("question-circle")), br()),
)
)
),
###############################################################
# 2. Filter and Normalize dataset
###############################################################
shinydashboard::tabItem(tabName = "filter_normalize",
fluidPage(
#Right Panel
column(width=7,
shinydashboard::box(title = tagList(shiny::icon("fas fa-filter", verify_fa = FALSE ), " Filter & Normalize"),
width = NULL, status="success", solidHeader=TRUE,
column(6, align="left",
column(12, align = "middle", h4("Cell coverage")),
br(), br(),
plotly::plotlyOutput("cell_coverage", height=250) %>%
shinycssloaders::withSpinner(type=8,color="#434C5E",size = 0.75),
br(), hr()),
column(6, align="left",
column(12, align = "middle", h4("Feature coverage")),
br(), br(),
plotly::plotlyOutput("feature_coverage", height=250) %>%
shinycssloaders::withSpinner(type=8,color="#434C5E",size = 0.75),
br(), hr()),
column(12, align="left",
uiOutput("table_QC_filt_box"),
br(), hr(),
uiOutput('min_coverage_cell_ui'),
uiOutput('quant_removal_ui'),
uiOutput('n_feature_UI'),
selectInput("norm_type", "Normalization method: ", choices = c("TFIDF", "CPM"), width = "20%"),
uiOutput("remove_PC_UI"),
checkboxInput("run_tsne", "Run T-SNE", value= FALSE) %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "run_tsne"),
checkboxInput("do_subsample", "Perform subsampling", value=FALSE)%>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "subsampling"),
uiOutput("do_subsample"),
checkboxInput("exclude_regions", "Exclude specific genomic regions", value=FALSE) %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "exclude_region"),
uiOutput("exclude_file"),
checkboxInput("do_batch_corr", "Perform batch correction", value=FALSE) %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "batch_correction"),
uiOutput("num_batches")),
column(5, align="left",
uiOutput("batch_names")),
column(7, align="left",
htmlOutput("batch_sel")),
column(12, align="left",
hr(),
actionButton("filter_normalize_reduce", "Filter, Normalize & Reduce")))),
column(width = 5,
shinydashboard::box(title=tagList(shiny::icon("file"), " Select filtered & normalized dataset"), width = NULL, status="success", solidHeader=TRUE,
column(12, align="left",
htmlOutput("selected_reduced_dataset"),
textOutput("red_data_selection_info"),
textOutput("red_data_selection_format")))
# uiOutput("cell_feature_coverage_after")
)
)
),
###############################################################
# 3. Vizualising cells in reduced dimension
###############################################################
shinydashboard::tabItem(
tabName = "vizualize_dim_red",
fluidPage(
column(width=6,
shinydashboard::box(title = tagList(shiny::icon("fas fa-image"), " PCA"), width = NULL, status="success", solidHeader=TRUE,
column(6, align="left", uiOutput("feature_color")),
column(12, align="left",plotOutput("pca_plot") %>%
shinycssloaders::withSpinner(type=8,color="#434C5E",size = 0.75) %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "pca_plot")
),
column(3, align="left", uiOutput("pc_select_x")),
column(3, align="left", uiOutput("pc_select_y"))),
uiOutput("contribution_to_pca_UI"),
uiOutput("correlation_to_pca_UI")),
column(width=6,
shinydashboard::box(title=tagList(shiny::icon("fas fa-image"), " UMAP"), width = NULL, status="success", solidHeader=TRUE,
column(12, align="left", plotOutput("UMAP_plot") %>%
shinycssloaders::withSpinner(type=8,color="#434C5E",size = 0.75) %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "umap_plot")
)),
uiOutput("tsne_box")
),
column(width=6, uiOutput("color_box"))
)
),
###############################################################
# 4. Consensus clustering on correlated cells
###############################################################
shinydashboard::tabItem(tabName = "cons_clustering",
fluidPage(
column(width=6,
shinydashboard::box(title=tagList(shiny::icon("cube")," Hierarchical Clustering"),
width=NULL, status="success", solidHeader=TRUE,
column(12, align ="center", plotOutput("hc_heatmap_plot", height=500, width=500) %>%
shinycssloaders::withSpinner(type=8,color="#434C5E",size = 0.75) %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "correlation_clustering"))
),
uiOutput("consensus_clustering_box"),
uiOutput("correlation_filtering_box")
),
column(width=6,
shinydashboard::box(title=tagList(shiny::icon("project-diagram"), "Cluster Cells"), width=NULL, status="success", solidHeader=TRUE,
align="left",
column(width=4, uiOutput("clustering_method_UI")),
column(width=4, uiOutput("clustering_UI")),
column(width=3, br(),br(), uiOutput("consensus_clustering_UI")),
column(width=3, br(),br(),actionButton(inputId = "choose_cluster", label = "Launch clustering"))
),
uiOutput("contingency_table_cluster"),
uiOutput("UMAP_box"),
uiOutput("IDclust_box"),
uiOutput("tsne_box_cf"),
uiOutput("color_box_cf"),
shinydashboard::box(title=tagList(shiny::icon("cube")," Hierarchical Clustering with cluster annotation"), width=NULL,
status="success", solidHeader=TRUE, align="left",
column(width=4,
actionButton(inputId = "do_annotated_heatmap_plot", label = "Plot Clustered Heatmap"), br()),
column(width=12, uiOutput("annotated_heatmap_UI"))
),
shinydashboard::box(title=tagList(shiny::icon("ruler-combined"), " Intra / Inter correlation"), width=NULL,
status="success", solidHeader=TRUE, align="left",
collapsible = TRUE, collapsed = TRUE,
column(12, align="left",
column(width=4,uiOutput("violin_color")),
column(width=4,checkboxInput("add_jitter", shiny::HTML("<b>Add single-cells</b>"), value= FALSE),
column(3, align = "left", actionButton(inputId = "save_plots_violins",
label = "Save HQ plots",
icon = icon("fas fa-image", verify_fa = FALSE))) %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "intra_inter_correlation")),
column(width=4,uiOutput("jitter_color")), br(),br(),br(),br(),br(),
mainPanel(tabsetPanel(id='inter_intra_cor',
tabPanel("Intracorrelation", column(width=12, uiOutput("intra_corr_UI")
)),
tabPanel("Intercorrelation", column(width=12, column(10, uiOutput("reference_group")),
br(), br(), br(), br(), br(),
uiOutput("inter_corr_UI")))
))),
)
)
)
),
###############################################################
# 5. Coverages [optional]
###############################################################
shinydashboard::tabItem(tabName = "coverage",
fluidPage(
column(width=4,
shinydashboard::box(title=tagList(shiny::icon("chart-area"), " Generate Coverage Plots"), width=NULL, status="success", solidHeader=TRUE,
column(12, align="left", htmlOutput("coverage_info"), hr()),
tags$style(HTML(".large_icon { font-size: 70px; }")),
column(12, align="left",
uiOutput("coverage_folder_ui"),
br(),hr(),br(),
uiOutput("coverage_upload")),
column(12, align="left", sliderInput(
inputId = "quantile_for_peak_calling", label = "Quantile of signal to define peak",
min = 0, max = 1, value = 0.85, step = 0.005)),
column(4, align="left", textInput(
inputId = "coverage_bin_size", label = "Resolution", value = 150)),
column(4, align="left", textInput(
inputId = "coverage_n_smoothBin", label = "Smoothing", value = 5)),
column(12, align="left", actionButton("do_coverage", "Create coverage & Call Peaks")))),
column(width=8, uiOutput("coverage_UI"),
uiOutput("coverage_plot_UI"))
)
),
###############################################################
# 6. Peak calling [optional]
###############################################################
# shinydashboard::tabItem(tabName = "peak_calling",
# fluidPage(
# column(width=6,
# shinydashboard::box(title=tagList(shiny::icon("fab fa-mountain", verify_fa = FALSE), " Peak calling"), width=NULL, status="success", solidHeader=TRUE,
# column(12, align="left", textOutput("peak_calling_info"), hr()),
# tags$style(HTML(".large_icon { font-size: 70px; }")),
# column(5, align="left",
# htmlOutput("peak_calling_system"), hr()),
# column(5,offset = 1,align="center", htmlOutput("peak_calling_icon")),
# column(12, align="left",
# sliderInput("peak_distance_to_merge", "Select distance of peaks to merge:", min=0, max=50000, value=5000, step=100),
# shinyFiles::shinyDirButton("pc_folder", "Browse folder of BAM / scBED files" ,
# icon = icon("folder-open"),
# title = "Please select a folder:",
# buttonType = "default", class = NULL),
# uiOutput("pc_upload")),
# br(), br(),
# column(4, align="left", textOutput("pc_k_selection"),
# selectInput("pc_stat","Select statistic for cutoff:", choices=c("p.value", "q.value"), selected="p.value")),
# column(12, align="left", br(), br(),
# sliderInput("pc_stat_value", "Select significance threshold:", min=0, max=0.25, value=0.05, step=0.01)),
# column(12, align="left", hr(), actionButton("do_pc", "Call peaks / Create Consensus Peaks"))))
# )
# ),
###############################################################
# 7. Differential analysis
###############################################################
shinydashboard::tabItem(tabName = "diff_analysis",
fluidPage(
column(width=5,
shinydashboard::box(title= tagList(shiny::icon("sort-amount-up"), " Run Differential Analysis"), width=NULL, status="success", solidHeader=TRUE,
column(12, align="left", textOutput("diff_analysis_info") %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "differential_analysis"), br()),
column(8, align="left", uiOutput("selected_k"), br(), br()),
column(5, align="left", selectInput("de_type", "Select type of comparison:",
choices=list("One vs Rest (activation)" = "one_vs_rest_fast",
"One vs Rest (classic)" = "one_vs_rest",
"Pairwise" = "pairwise",
"Custom" = "custom"))),
column(2, offset = 0,align="left"),
column(4, align="left", selectInput("da_method", "Select method:",
choices=list("Wilcoxon" = "wilcox",
"edgeR GLM" = "neg.binomial"))),
column(6, align="left", offset = 0, uiOutput("name_group")),
column(6, align="left", offset = 0, uiOutput("name_ref")),
column(3, align="left", offset = 0, uiOutput("da_group")),
column(3, align="left", offset = 0, uiOutput("group_choice")),
column(1, align="left", offset = 0, uiOutput("text_vs")),
column(2, align="left", offset = 0, uiOutput("custom_da_ref")),
column(3, align="left", offset = 0, uiOutput("ref_choice")),
column(12, align="left", hr(), actionButton("run_DA", "Start analysis"))),
uiOutput("da_summary_box")),
column(width=7,
shinydashboard::box(title= tagList(shiny::icon("bullseye"), " Find Significantly Differential Features"), width=NULL, status="success", solidHeader=TRUE,
column(8, align="left", htmlOutput("selected_DA_GSA_dataset")),
column(8, align="left",
shinyWidgets::sliderTextInput(inputId = "qval.th", label = "Adjusted p-value to select significant features:",
choices = c(1e-10, 1e-9, 1e-8, 1e-7, 1e-6, 1e-5, 1e-4, 1e-3, 0.0001, 0.001, 0.01, 0.02, 0.03, 0.04, 0.04, 0.05, 0.1, 0.15, 0.20, 0.25),
selected = 0.01, grid = TRUE),
sliderInput("logFC.th", "Minimum log-fold change to select significant locations:", min=0, max=3, value=1, step=0.01),
sliderInput("min.percent", "Minimum fraction of active cells in feature:", min=0, max=0.5, value=0.01, step=0.005)),
column(4, align="center", br(), br(), br(),br(), br(), br(),
shiny::actionButton("apply_DA_filters", label = "Apply filters"))),
uiOutput("da_visu_box")))
),
###############################################################
# 8. Enrichment analysis
###############################################################
shinydashboard::tabItem(tabName = "enrich_analysis",
fluidPage(
column(width=6,
shinydashboard::box(title=tagList(shiny::icon("code-branch"), " Gene Set Analysis"), width=NULL, status="success", solidHeader=TRUE,
column(12, align="left", htmlOutput("enr_info"), br(),
uiOutput("use_peaks"),
actionButton("do_enrich", "Start enrichment analysis"))),
shinydashboard::box(title=tagList(icon("th"), " Enriched Gene sets in differential features"), width=NULL, status="success", solidHeader=TRUE,
column(4, align="left", uiOutput("GSA_group_sel"), br()),
column(8, align="left", uiOutput("enr_class_sel"), br()),
column(8, align="left", sliderInput("pathway_size_GSA", label = "Select pathway size",
min = 1, max = 2500, value = c(25, 1000), step = 1), br()),
column(12, align="left",
mainPanel(tabsetPanel(id='enr_tables',
tabPanel("In differential features", div(style = 'overflow-x: scroll', DT::dataTableOutput('all_enrich_table'))),
tabPanel("In enriched features", div(style = 'overflow-x: scroll', DT::dataTableOutput('over_enrich_table'))),
tabPanel("In depleted features", div(style = 'overflow-x: scroll', DT::dataTableOutput('under_enrich_table')))), width=12),
br(), br(), br(), br(), br(),
downloadButton("download_enr_data", "Download tables")))),
column(width=6,
shinydashboard::box(title=tagList(icon("image"), " UMAP of enrichment near TSS"), width=NULL, status="success", solidHeader=TRUE,
column(3, align="left", uiOutput("gene_sel")),
column(3, align="left", checkboxInput("label_cluster_umap_GSA", "Label cluster", value = T) ),
column(3, align="left", selectInput("color_by_violin_GSA", "Color by", choices = c("cell_cluster","sample_id")) ),
column(3, align="left", actionButton("save_plot_GSA", "Save HQ plot")),
column(12, align="left", uiOutput("gene_umap_UI")), br(),
column(12, align="left", uiOutput("gene_violin_UI"))
),
shinydashboard::box(title=tagList(icon("image"), " Enrichment in Gene Sets"), width=NULL, status="success", solidHeader=TRUE,
column(4, align="left", actionButton("plot_pathways", "Plot pathways")),
column(8, align="left", uiOutput("pathways_sel")),
column(12, align="left",uiOutput("pathways_umap_UI"))
)
))
),
###############################################################
# 8. TF analysis
###############################################################
shinydashboard::tabItem(tabName = "TF_analysis",
fluidPage(
column(width=6,
shinydashboard::box(title=tagList(shiny::icon("bezier-curve"), " Transcription Factor Analysis using ChEA3"), width=NULL, status="success", solidHeader=TRUE,
column(12, align="left", htmlOutput("TF_info"), br(),
uiOutput("use_peaks_TF"),
actionButton("do_enrich_TF", "Start TF enrichment analysis"))),
shinydashboard::box(title=tagList(icon("th"), " Enriched TF in differential features"), width=NULL, status="success", solidHeader=TRUE,
column(4, align="left", uiOutput("TF_group_sel"), br()),
column(12, align="left",
mainPanel(tabsetPanel(id='enr_tables_TF',
tabPanel("In differential features", div(style = 'overflow-x: scroll', DT::dataTableOutput('all_enrich_table_TF'))),
tabPanel("In enriched features", div(style = 'overflow-x: scroll', DT::dataTableOutput('over_enrich_table_TF'))),
tabPanel("In depleted features", div(style = 'overflow-x: scroll', DT::dataTableOutput('under_enrich_table_TF')))), width=12),
br(), br(), br(), br(), br(),
downloadButton("download_enr_data_TF", "Download tables"))),
),
column(width=6, uiOutput("TF_results_UI"))
)
),
###############################################################
# 9. Close app
###############################################################
shinydashboard::tabItem(tabName="close_and_save",
fluidPage(shinyjs::useShinyjs(),
# extendShinyjs(text = jscode, functions = c("closeWindow")),
column(width=6,
shinydashboard::box(title='Close App & Save Analysis', solidHeader=TRUE, status='danger', width=NULL,
column(12, actionButton("generate_report", "Generate HTML Report")), br(), br(),
column(12, actionButton("close_and_save", "Close App & Save Analysis"))
)
),
column(width=6,
shinydashboard::box(title="Delete analysis", width = NULL, status="success", solidHeader=TRUE,
column(9, align="left", uiOutput("selected_delete_analysis")),
column(3, align="left", br(), actionButton("delete_analysis", "Delete")),
column(12, align="left", textOutput("analysis_deletion_info")))),
)
)
)))
)
vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(shiny)
library(shinyjs)
library(dplyr)
mytheme <- fresh::create_theme(
fresh::adminlte_color(
light_blue = "#434C5E",
red = "#D81B60",
green = "#434C5E",
yellow = "#f39c12",
aqua = "#39CCCC"
),
fresh::adminlte_sidebar(
dark_bg = "#D8DEE9",
dark_hover_bg = "#81A1C1",
dark_color = "#2E3440"),
fresh::adminlte_global(
content_bg = "#FFF",
)
)
shinyUI(shinydashboardPlus::dashboardPage(freshTheme = mytheme,
header = shinydashboardPlus::dashboardHeader(
title = tagList(
span(class = "logo-lg", "ChromSCape"),
icon("ellipsis-h")),
leftUi = tagList(uiOutput("dropdown_feature_select_ui"),
br(),
br(),
uiOutput("download_scExp_UI"))
),
sidebar = shinydashboardPlus::dashboardSidebar(
shinydashboard::sidebarUserPanel(
"Vallot Lab",
subtitle = a(href = "https://github.com/vallotlab/ChromSCape/", icon("github"), "GitHub"),
image = "LogoCurie.png"
),
shinydashboard::sidebarMenu(id="tabs",
shinydashboard::menuItem("Select & Import", tabName = "select_import", icon=icon("upload")),
shinydashboard::menuItem("Filter & Normalize", tabName = "filter_normalize", icon=icon("fas fa-filter", verify_fa = FALSE)),
shinydashboard::menuItem("Visualize Cells", tabName = "vizualize_dim_red", icon=icon("fas fa-image")),
shinydashboard::menuItem("Cluster Cells", tabName = "cons_clustering", icon=icon("th")),
shinydashboard::menuItem("Coverage & Peak Calling", tabName = "coverage", icon=icon("chart-area")),
shinydashboard::menuItem("Differential Analysis", tabName = "diff_analysis", icon=icon("sort-amount-up")),
shinydashboard::menuItem("Gene Set Analysis", tabName = "enrich_analysis", icon=icon("code-branch")),
shinydashboard::menuItem("TF analysis", tabName = "TF_analysis", icon=icon("bezier-curve")),
shinydashboard::menuItem("Generate Report & Close App", tabName = "close_and_save", icon=icon("close", verify_fa = FALSE)),
shinydashboard::menuItem(
badgeColor = "green",
expandedName = "hello",
startExpanded = TRUE,
" ", column(width = 12, actionButton("popupUMAP", width = "70%", class = "btn-default",
label = "UMAP", icon = icon("fas fa-image")))
)
)
),
controlbar = shinydashboardPlus::dashboardControlbar(
id = "controlbar",
shinydashboardPlus::controlbarMenu(
id = "menu",
shinydashboardPlus::controlbarItem(
title = "Visualisation Settings",
icon = icon("chart-bar"),
h4("UMAP"), br(),
sliderInput("options.dotplot_downsampling", "Downsampled cells",
min = 500, max = 100000, step = 10, value = getOption("ChromSCape_options")$dotplot_downsample),
sliderInput("options.dotplot_size", "Point size",
min = 0.01, max = 5, step = 0.01, value = getOption("ChromSCape_options")$dotplot_size),
sliderInput("options.dotplot_transparency", "Point transparency",
min = 0.01, max = 1, step = 0.01, value = getOption("ChromSCape_options")$dotplot_transparency),
sliderInput("options.dotplot_max_distanceToTSS", "Max. distance to TSS",
min = 0, max = 100000, step = 100, value = getOption("ChromSCape_options")$dotplot_max_distanceToTSS),
sliderInput("options.dotplot_min_quantile", "Remove lower range outlier",
min = 0, max = 1, step = 0.01, value = getOption("ChromSCape_options")$dotplot_min_quantile),
sliderInput("options.dotplot_max_quantile", "Remove higher range outlier",
min = 0, max = 1, step = 0.01, value = getOption("ChromSCape_options")$dotplot_max_quantile),
h4("Heatmap"), br(),
sliderInput("options.heatmap_downsampling", "Downsampled cells",
min = 500, max = 20000, step = 10, value = getOption("ChromSCape_options")$heatmap_downsample)
),
shinydashboardPlus::controlbarItem(
title = "Parallel Settings",
icon = icon("align-left"),
selectInput("options.nb_workers","Select number of workers for parallel computation",
choices= seq_len(future::availableCores()), selected = BiocParallel::bpworkers(BiocParallel::bpparam())),
selectInput("options.bpparam_class","Select parallel computation type",
choices = names(BiocParallel::registered()), selected = 1)
)
)
),
body = shinydashboard::dashboardBody(
shinyjs::useShinyjs(),
tags$head(tags$link(rel="shortcut icon", href="ChromSCape_logo.png")),
tags$head(includeCSS('www/style.css')),
tags$head(includeCSS('www/introjs.min.css')),
tags$head(includeCSS('www/app.css')),
tags$style(type="text/css",
".shiny-output-error { visibility: hidden; }",
".shiny-output-error:before { visibility: hidden; }"
),
tags$head(tags$style(HTML(
'.myClass {
font-size: 20px;
line-height: 50px;
text-align: left;
font-family: "Helvetica Neue",Helvetica,Arial,sans-serif;
padding: 0 15px;
overflow: hidden;
color: white;
}
'))),
tags$script(HTML('
$(document).ready(function() {
$("header").find("nav").append(\'<div id="pageHeader" class="myClass"></div>\');
})
')),
shinydashboard::tabItems(
###############################################################
# 1. Select Analysis & Import dataset
###############################################################
shinydashboard::tabItem(tabName = "select_import",
fluidPage(
# Add ressources for UX
shiny::includeScript(file.path(system.file(package="ChromSCape"),"js.cookie.js")),
shiny::includeScript(file.path(system.file(package="ChromSCape"),"intro.min.js")),
shiny::includeScript(file.path(system.file(package="ChromSCape"),"app.js")),
shiny::includeScript(file.path(system.file(package="ChromSCape"),"www","shiny_js_functions.js")),
shinyWidgets::chooseSliderSkin("Flat", color = "#112446"),
#Load shinyJS added functions
shinyjs::extendShinyjs(script = file.path(system.file(package="ChromSCape"),"www","shiny_js_functions.js"),
functions = c("init_directory","save_cookie","disableTab","enableTab")),
#Center Panel
column(width=6,align="left",
shinydashboard::box(title=tagList(shiny::icon("folder"), " Select output directory"), width = NULL, status="success",
solidHeader=TRUE,
column(12, align="left",
shinyFiles::shinyDirButton("data_folder", icon = icon("folder-open"), label = "Browse", title = "Upload") %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "output_directory"), br(),
verbatimTextOutput("directory", placeholder = TRUE)),
column(12, align="left", textOutput("data_folder_info"))),
shinydashboard::box(title=tagList(shiny::icon("upload"), " Import raw data & Create new analysis"), width = NULL, status="success", solidHeader=TRUE,
column(8, br()) %>%
shinyhelper::helper(type = 'markdown', colour = "#E6C717", icon = "question-circle",
content = "HistoneMark_recommandations"),
column(12, align="left",
column(12, align="left",textInput("new_analysis_name", "Enter a name for the new analysis :", value = "Analysis_1"),
selectInput("annotation","Select reference genome:", choices=c("hg38", "mm10", "ce11")),
textOutput("data_matrices_info") %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "datamatrix_input")),
column(6,
radioButtons("data_choice_box", label = "Input data type",
choices = list("Dense Matrix"="DenseMatrix",
"Sparse Matrix" = "SparseMatrix",
"Fragment File" = "FragmentFile",
"Single-cell BAM files" = "scBAM",
"Single-cell BED files" = "scBED"
))),
column(6,
uiOutput("input_data_ui")),
column(12,
uiOutput("advanced_data_input")),
column(3, uiOutput("rebin_matrices_checkbox_ui") %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "rebin_matrices")) ,
column(12,uiOutput("rebin_matrices_ui")),
column(3, actionButton("create_analysis", "Create analysis")),
column(4, uiOutput("add_to_current_analysis_checkbox_UI"))
))
),
column(6,
column(11, align="left",
shinydashboard::box(title=tagList(shiny::icon("file"), " Current analysis"), width = NULL, status="success", solidHeader=TRUE,
column(12, align="left",
uiOutput("selected_analysis")
)),
uiOutput("rename_file_box")),
column(1, actionButton("startHelp","Help", icon = icon("question-circle")), br()),
)
)
),
###############################################################
# 2. Filter and Normalize dataset
###############################################################
shinydashboard::tabItem(tabName = "filter_normalize",
fluidPage(
#Right Panel
column(width=7,
shinydashboard::box(title = tagList(shiny::icon("fas fa-filter", verify_fa = FALSE ), " Filter & Normalize"),
width = NULL, status="success", solidHeader=TRUE,
column(6, align="left",
column(12, align = "middle", h4("Cell coverage")),
br(), br(),
plotly::plotlyOutput("cell_coverage", height=250) %>%
shinycssloaders::withSpinner(type=8,color="#434C5E",size = 0.75),
br(), hr()),
column(6, align="left",
column(12, align = "middle", h4("Feature coverage")),
br(), br(),
plotly::plotlyOutput("feature_coverage", height=250) %>%
shinycssloaders::withSpinner(type=8,color="#434C5E",size = 0.75),
br(), hr()),
column(12, align="left",
uiOutput("table_QC_filt_box"),
br(), hr(),
uiOutput('min_coverage_cell_ui'),
uiOutput('quant_removal_ui'),
uiOutput('n_feature_UI'),
selectInput("norm_type", "Normalization method: ", choices = c("TFIDF", "CPM"), width = "20%"),
uiOutput("remove_PC_UI"),
checkboxInput("run_tsne", "Run T-SNE", value= FALSE) %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "run_tsne"),
checkboxInput("do_subsample", "Perform subsampling", value=FALSE)%>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "subsampling"),
uiOutput("do_subsample"),
checkboxInput("exclude_regions", "Exclude specific genomic regions", value=FALSE) %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "exclude_region"),
uiOutput("exclude_file"),
checkboxInput("do_batch_corr", "Perform batch correction", value=FALSE) %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "batch_correction"),
uiOutput("num_batches")),
column(5, align="left",
uiOutput("batch_names")),
column(7, align="left",
htmlOutput("batch_sel")),
column(12, align="left",
hr(),
actionButton("filter_normalize_reduce", "Filter, Normalize & Reduce")))),
column(width = 5,
shinydashboard::box(title=tagList(shiny::icon("file"), " Select filtered & normalized dataset"), width = NULL, status="success", solidHeader=TRUE,
column(12, align="left",
htmlOutput("selected_reduced_dataset"),
textOutput("red_data_selection_info"),
textOutput("red_data_selection_format")))
# uiOutput("cell_feature_coverage_after")
)
)
),
###############################################################
# 3. Vizualising cells in reduced dimension
###############################################################
shinydashboard::tabItem(
tabName = "vizualize_dim_red",
fluidPage(
column(width=6,
shinydashboard::box(title = tagList(shiny::icon("fas fa-image"), " PCA"), width = NULL, status="success", solidHeader=TRUE,
column(6, align="left", uiOutput("feature_color")),
column(12, align="left",plotOutput("pca_plot") %>%
shinycssloaders::withSpinner(type=8,color="#434C5E",size = 0.75) %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "pca_plot")
),
column(3, align="left", uiOutput("pc_select_x")),
column(3, align="left", uiOutput("pc_select_y"))),
uiOutput("contribution_to_pca_UI"),
uiOutput("correlation_to_pca_UI")),
column(width=6,
shinydashboard::box(title=tagList(shiny::icon("fas fa-image"), " UMAP"), width = NULL, status="success", solidHeader=TRUE,
column(12, align="left", plotOutput("UMAP_plot") %>%
shinycssloaders::withSpinner(type=8,color="#434C5E",size = 0.75) %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "umap_plot")
)),
uiOutput("tsne_box")
),
column(width=6, uiOutput("color_box"))
)
),
###############################################################
# 4. Consensus clustering on correlated cells
###############################################################
shinydashboard::tabItem(tabName = "cons_clustering",
fluidPage(
column(width=6,
shinydashboard::box(title=tagList(shiny::icon("cube")," Hierarchical Clustering"),
width=NULL, status="success", solidHeader=TRUE,
column(12, align ="center", plotOutput("hc_heatmap_plot", height=500, width=500) %>%
shinycssloaders::withSpinner(type=8,color="#434C5E",size = 0.75) %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "correlation_clustering"))
),
uiOutput("consensus_clustering_box"),
uiOutput("correlation_filtering_box")
),
column(width=6,
shinydashboard::box(title=tagList(shiny::icon("project-diagram"), "Cluster Cells"), width=NULL, status="success", solidHeader=TRUE,
align="left",
column(width=4, uiOutput("clustering_method_UI")),
column(width=4, uiOutput("clustering_UI")),
column(width=3, br(),br(), uiOutput("consensus_clustering_UI")),
column(width=3, br(),br(),actionButton(inputId = "choose_cluster", label = "Launch clustering"))
),
uiOutput("contingency_table_cluster"),
uiOutput("UMAP_box"),
uiOutput("IDclust_box"),
uiOutput("tsne_box_cf"),
uiOutput("color_box_cf"),
shinydashboard::box(title=tagList(shiny::icon("cube")," Hierarchical Clustering with cluster annotation"), width=NULL,
status="success", solidHeader=TRUE, align="left",
column(width=4,
actionButton(inputId = "do_annotated_heatmap_plot", label = "Plot Clustered Heatmap"), br()),
column(width=12, uiOutput("annotated_heatmap_UI"))
),
shinydashboard::box(title=tagList(shiny::icon("ruler-combined"), " Intra / Inter correlation"), width=NULL,
status="success", solidHeader=TRUE, align="left",
collapsible = TRUE, collapsed = TRUE,
column(12, align="left",
column(width=4,uiOutput("violin_color")),
column(width=4,checkboxInput("add_jitter", shiny::HTML("<b>Add single-cells</b>"), value= FALSE),
column(3, align = "left", actionButton(inputId = "save_plots_violins",
label = "Save HQ plots",
icon = icon("fas fa-image", verify_fa = FALSE))) %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "intra_inter_correlation")),
column(width=4,uiOutput("jitter_color")), br(),br(),br(),br(),br(),
mainPanel(tabsetPanel(id='inter_intra_cor',
tabPanel("Intracorrelation", column(width=12, uiOutput("intra_corr_UI")
)),
tabPanel("Intercorrelation", column(width=12, column(10, uiOutput("reference_group")),
br(), br(), br(), br(), br(),
uiOutput("inter_corr_UI")))
))),
)
)
)
),
###############################################################
# 5. Coverages [optional]
###############################################################
shinydashboard::tabItem(tabName = "coverage",
fluidPage(
column(width=4,
shinydashboard::box(title=tagList(shiny::icon("chart-area"), " Generate Coverage Plots"), width=NULL, status="success", solidHeader=TRUE,
column(12, align="left", htmlOutput("coverage_info"), hr()),
tags$style(HTML(".large_icon { font-size: 70px; }")),
column(12, align="left",
uiOutput("coverage_folder_ui"),
br(),hr(),br(),
uiOutput("coverage_upload")),
column(12, align="left", sliderInput(
inputId = "quantile_for_peak_calling", label = "Quantile of signal to define peak",
min = 0, max = 1, value = 0.85, step = 0.005)),
column(4, align="left", textInput(
inputId = "coverage_bin_size", label = "Resolution", value = 150)),
column(4, align="left", textInput(
inputId = "coverage_n_smoothBin", label = "Smoothing", value = 5)),
column(12, align="left", actionButton("do_coverage", "Create coverage & Call Peaks")))),
column(width=8, uiOutput("coverage_UI"),
uiOutput("coverage_plot_UI"))
)
),
###############################################################
# 6. Peak calling [optional]
###############################################################
# shinydashboard::tabItem(tabName = "peak_calling",
# fluidPage(
# column(width=6,
# shinydashboard::box(title=tagList(shiny::icon("fab fa-mountain", verify_fa = FALSE), " Peak calling"), width=NULL, status="success", solidHeader=TRUE,
# column(12, align="left", textOutput("peak_calling_info"), hr()),
# tags$style(HTML(".large_icon { font-size: 70px; }")),
# column(5, align="left",
# htmlOutput("peak_calling_system"), hr()),
# column(5,offset = 1,align="center", htmlOutput("peak_calling_icon")),
# column(12, align="left",
# sliderInput("peak_distance_to_merge", "Select distance of peaks to merge:", min=0, max=50000, value=5000, step=100),
# shinyFiles::shinyDirButton("pc_folder", "Browse folder of BAM / scBED files" ,
# icon = icon("folder-open"),
# title = "Please select a folder:",
# buttonType = "default", class = NULL),
# uiOutput("pc_upload")),
# br(), br(),
# column(4, align="left", textOutput("pc_k_selection"),
# selectInput("pc_stat","Select statistic for cutoff:", choices=c("p.value", "q.value"), selected="p.value")),
# column(12, align="left", br(), br(),
# sliderInput("pc_stat_value", "Select significance threshold:", min=0, max=0.25, value=0.05, step=0.01)),
# column(12, align="left", hr(), actionButton("do_pc", "Call peaks / Create Consensus Peaks"))))
# )
# ),
###############################################################
# 7. Differential analysis
###############################################################
shinydashboard::tabItem(tabName = "diff_analysis",
fluidPage(
column(width=5,
shinydashboard::box(title= tagList(shiny::icon("sort-amount-up"), " Run Differential Analysis"), width=NULL, status="success", solidHeader=TRUE,
column(12, align="left", textOutput("diff_analysis_info") %>%
shinyhelper::helper(type = 'markdown', colour = "#434C5E", icon ="info-circle",
content = "differential_analysis"), br()),
column(8, align="left", uiOutput("selected_k"), br(), br()),
column(5, align="left", selectInput("de_type", "Select type of comparison:",
choices=list("One vs Rest (activation)" = "one_vs_rest_fast",
"One vs Rest (classic)" = "one_vs_rest",
"Pairwise" = "pairwise",
"Custom" = "custom"))),
column(2, offset = 0,align="left"),
column(4, align="left", selectInput("da_method", "Select method:",
choices=list("Wilcoxon" = "wilcox",
"edgeR GLM" = "neg.binomial"))),
column(6, align="left", offset = 0, uiOutput("name_group")),
column(6, align="left", offset = 0, uiOutput("name_ref")),
column(3, align="left", offset = 0, uiOutput("da_group")),
column(3, align="left", offset = 0, uiOutput("group_choice")),
column(1, align="left", offset = 0, uiOutput("text_vs")),
column(2, align="left", offset = 0, uiOutput("custom_da_ref")),
column(3, align="left", offset = 0, uiOutput("ref_choice")),
column(12, align="left", hr(), actionButton("run_DA", "Start analysis"))),
uiOutput("da_summary_box")),
column(width=7,
shinydashboard::box(title= tagList(shiny::icon("bullseye"), " Find Significantly Differential Features"), width=NULL, status="success", solidHeader=TRUE,
column(8, align="left", htmlOutput("selected_DA_GSA_dataset")),
column(8, align="left",
shinyWidgets::sliderTextInput(inputId = "qval.th", label = "Adjusted p-value to select significant features:",
choices = c(1e-10, 1e-9, 1e-8, 1e-7, 1e-6, 1e-5, 1e-4, 1e-3, 0.0001, 0.001, 0.01, 0.02, 0.03, 0.04, 0.04, 0.05, 0.1, 0.15, 0.20, 0.25),
selected = 0.01, grid = TRUE),
sliderInput("logFC.th", "Minimum log-fold change to select significant locations:", min=0, max=3, value=1, step=0.01),
sliderInput("min.percent", "Minimum fraction of active cells in feature:", min=0, max=0.5, value=0.01, step=0.005)),
column(4, align="center", br(), br(), br(),br(), br(), br(),
shiny::actionButton("apply_DA_filters", label = "Apply filters"))),
uiOutput("da_visu_box")))
),
###############################################################
# 8. Enrichment analysis
###############################################################
shinydashboard::tabItem(tabName = "enrich_analysis",
fluidPage(
column(width=6,
shinydashboard::box(title=tagList(shiny::icon("code-branch"), " Gene Set Analysis"), width=NULL, status="success", solidHeader=TRUE,
column(12, align="left", htmlOutput("enr_info"), br(),
uiOutput("use_peaks"),
actionButton("do_enrich", "Start enrichment analysis"))),
shinydashboard::box(title=tagList(icon("th"), " Enriched Gene sets in differential features"), width=NULL, status="success", solidHeader=TRUE,
column(4, align="left", uiOutput("GSA_group_sel"), br()),
column(8, align="left", uiOutput("enr_class_sel"), br()),
column(8, align="left", sliderInput("pathway_size_GSA", label = "Select pathway size",
min = 1, max = 2500, value = c(25, 1000), step = 1), br()),
column(12, align="left",
mainPanel(tabsetPanel(id='enr_tables',
tabPanel("In differential features", div(style = 'overflow-x: scroll', DT::dataTableOutput('all_enrich_table'))),
tabPanel("In enriched features", div(style = 'overflow-x: scroll', DT::dataTableOutput('over_enrich_table'))),
tabPanel("In depleted features", div(style = 'overflow-x: scroll', DT::dataTableOutput('under_enrich_table')))), width=12),
br(), br(), br(), br(), br(),
downloadButton("download_enr_data", "Download tables")))),
column(width=6,
shinydashboard::box(title=tagList(icon("image"), " UMAP of enrichment near TSS"), width=NULL, status="success", solidHeader=TRUE,
column(3, align="left", uiOutput("gene_sel")),
column(3, align="left", checkboxInput("label_cluster_umap_GSA", "Label cluster", value = T) ),
column(3, align="left", selectInput("color_by_violin_GSA", "Color by", choices = c("cell_cluster","sample_id")) ),
column(3, align="left", actionButton("save_plot_GSA", "Save HQ plot")),
column(12, align="left", uiOutput("gene_umap_UI")), br(),
column(12, align="left", uiOutput("gene_violin_UI"))
),
shinydashboard::box(title=tagList(icon("image"), " Enrichment in Gene Sets"), width=NULL, status="success", solidHeader=TRUE,
column(4, align="left", actionButton("plot_pathways", "Plot pathways")),
column(8, align="left", uiOutput("pathways_sel")),
column(12, align="left",uiOutput("pathways_umap_UI"))
)
))
),
###############################################################
# 8. TF analysis
###############################################################
shinydashboard::tabItem(tabName = "TF_analysis",
fluidPage(
column(width=6,
shinydashboard::box(title=tagList(shiny::icon("bezier-curve"), " Transcription Factor Analysis using ChEA3"), width=NULL, status="success", solidHeader=TRUE,
column(12, align="left", htmlOutput("TF_info"), br(),
uiOutput("use_peaks_TF"),
actionButton("do_enrich_TF", "Start TF enrichment analysis"))),
shinydashboard::box(title=tagList(icon("th"), " Enriched TF in differential features"), width=NULL, status="success", solidHeader=TRUE,
column(4, align="left", uiOutput("TF_group_sel"), br()),
column(12, align="left",
mainPanel(tabsetPanel(id='enr_tables_TF',
tabPanel("In differential features", div(style = 'overflow-x: scroll', DT::dataTableOutput('all_enrich_table_TF'))),
tabPanel("In enriched features", div(style = 'overflow-x: scroll', DT::dataTableOutput('over_enrich_table_TF'))),
tabPanel("In depleted features", div(style = 'overflow-x: scroll', DT::dataTableOutput('under_enrich_table_TF')))), width=12),
br(), br(), br(), br(), br(),
downloadButton("download_enr_data_TF", "Download tables"))),
),
column(width=6, uiOutput("TF_results_UI"))
)
),
###############################################################
# 9. Close app
###############################################################
shinydashboard::tabItem(tabName="close_and_save",
fluidPage(shinyjs::useShinyjs(),
# extendShinyjs(text = jscode, functions = c("closeWindow")),
column(width=6,
shinydashboard::box(title='Close App & Save Analysis', solidHeader=TRUE, status='danger', width=NULL,
column(12, actionButton("generate_report", "Generate HTML Report")), br(), br(),
column(12, actionButton("close_and_save", "Close App & Save Analysis"))
)
),
column(width=6,
shinydashboard::box(title="Delete analysis", width = NULL, status="success", solidHeader=TRUE,
column(9, align="left", uiOutput("selected_delete_analysis")),
column(3, align="left", br(), actionButton("delete_analysis", "Delete")),
column(12, align="left", textOutput("analysis_deletion_info")))),
)
)
)))
)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.