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ui.R
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#
# ########################## #
#
# Loading libraries
#
# ########################## #
#
# library(graphics)
#library(pheatmap)
library(randomcoloR)
library(shiny)
library(shinyBS)
library(shinysky)
library(shinyjs)
library(V8)
library(shinythemes)
library(plotly)
library(shinyWidgets)
library(shinydashboard)
library(limma)
library(heatmaply)
library(ggplot2)
library(ggsignif)
library(RColorBrewer)
library(randomForest)
library(GenVisR)
library(doBy)
library(parallel)
library(caret)
library(survival)
library(survminer)
library(Cairo)
library(DT)
# setwd("/srv/shiny-server/CNApp/")
dashboardPage(title="CNApp - Copy Number Alterations Integrative Analysis",
#theme = shinytheme("paper"),
#shinythemes::themeSelector(), # easy select shiny themes (comment when selection is set!!!)
dashboardHeader(
title=HTML("<h2 style='text-align:left;margin:5px 0 0 20px'>CNApp</h2> <img style='margin:-60px 0 0 50px' src='ITEMS/imatges/chrom_cnapp.png' width='40%' heigth='40%'>"),
dropdownMenu(type="messages", icon=icon("home"), headerText = "", badgeStatus = NULL,
messageItem(icon=icon("home"), href="https://tools.idibaps.org/CNApp/home.html",
from= tags$div(tags$h4("CNApp web page")),
message=HTML("")
)
),
dropdownMenu(type="messages", icon=icon("info-circle"), headerText = "", badgeStatus = NULL,
messageItem(icon=icon("info-circle"), href="https://tools.idibaps.org/CNApp/#about",
from= tags$div(tags$h4("About CNApp")),
message=HTML("")
)
),
dropdownMenu(type="messages", icon=icon("github"), headerText = "", badgeStatus = NULL,
messageItem(icon=icon("github"), href="https://github.com/ait5/CNApp",
from= tags$div(tags$h4("github.com/ait5/CNApp")),
message=HTML("")
)
),
dropdownMenu(type="messages", icon=icon("refresh"), headerText = "CNApp will refresh and lose your session...", badgeStatus = NULL,
messageItem(icon=icon("exclamation-triangle"), href=NULL,
from= tags$div(tags$h4("Are you sure?"),br()),
message=actionBttn("clear", "Yes, clear all!", style="simple", size="sm", color="primary")
)
)
),
######dashboardSidebar#######
dashboardSidebar(div(id="dashboard_sidebar", style="position:fixed; margin: 0 5px 0 5px; width: 220px; min-width: 200px; background-color:#253744;",
div(id="body_sidebar",
sidebarMenu(
menuItem(text = div(HTML("<i class='fa fa-desktop' style='color:white'></i>   HOME       ")), tabName="wellcome_tab"),
menuItem(text = div(HTML("<i class='fa fa-folder-open' style='color:white'></i>   LOAD DATA       ")), tabName="load_data")
),
sidebarMenuOutput("side_menu_cin"),
sidebarMenuOutput("side_menu_cin.1"),
sidebarMenuOutput("side_menu_profiling"),
sidebarMenuOutput("side_menu_profiling.1"),
sidebarMenuOutput("side_menu_model")
# div(style = "position: fixed; overflow: visible; padding-top:15em;", sidebarMenuOutput("side_menu_create_model")),
# div(style = "position: fixed; overflow: visible; padding-top:15em;", sidebarMenuOutput("side_menu_my_model"))
),
div(id="footer", style="margin-left: 0px; margin-bottom: 0px; text-align: center; position: absolute; top:425px; background-color:#253744; padding: 50px 0 20px 0;",
HTML("
<a href='http://www.idibaps.org/' class='icons'><img src='ITEMS/imatges/sidebar/IDIBAPS1.png', alt='idibaps-image-link', width='150px', height='50px'></img></a>
<br><br><br>
<a href='http://www.ciberehd.org/' class='icons'><img src='ITEMS/imatges/sidebar/ciberehd.png', alt='ciberehd-image-link', width='150px', height='50px'></img></a>
<br><br><br>
<p class='copyright'>© CNApp web application. Designed by <a href=''>Sebastià Franch</a></p>.
")
)
#includeHTML("www/en/sidebar_page.html")
)),
##########dashboardBody#############
dashboardBody(
HTML("<script async src='https://www.googletagmanager.com/gtag/js?id=UA-121173624-1'></script><script>window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-121173624-1');</script>"
),
useShinyjs(),
tabItems(
######Tab WELCOME PAGE######
tabItem(tabName="wellcome_tab",
includeHTML("www/en/wellcome_page.html")
), #tabName="load_data"
######Tab LOAD DATA######
tabItem(tabName="load_data",
fluidRow(
column(4,fileInput("data_browse", "Load your data", width="100%",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv",
".bed",
".tsv",
".txt/tab-separeted-values"),
buttonLabel = "Browse")
),
column(1,
div(style="position:relative; top:2.5em; text-align:left;", title="empty data", actionLink("empty", label=icon("trash", "fa-1x")))
),
column(2,
br(),
div(style="text-align:left;", checkboxInput("use_demo", "Demo data", value=F))
),
column(1),
column(2,
#Help menu for format of input file
div(style="text-align:right;", actionLink("helpformat","Help", icon=icon("question-circle-o"))),
bsModal("modal","HELP: Input file","helpformat", includeHTML("./aux_files/help_with_input.html"))
)
),
fluidRow(
column(9,
# File specifications panel
uiOutput("file_specifics"),
textOutput('error_demo_read'),
tags$head(tags$style("#error_demo_read{color: red;
font-size: 10px;
font-style: italic;
}"
)
),
textOutput('error_reading_data'),
uiOutput('error_too_many_samples'),
textOutput('error_reading_annot_data'),
tags$head(tags$style("#error_reading_data{color: red;
font-size: 10px;
font-style: italic;
}"
)
),
br(),
uiOutput("go_to_funs")
)
),
br(),
hr(),
uiOutput("summary_data_MAIN"),
uiOutput("dim_data"),
verbatimTextOutput("summary_data")
), #tabName="load_data"
########Tab PARAM CIN########
tabItem(tabName="user_param_cin",
HTML("<h3><i class='fa fa-star' style='color:orange'></i>   RE-SEG & SCORE</h3>"),
br(),
div(id="USER_PARAM_cin",
div(style="text-align:right;", uiOutput("help_param_cin")),
uiOutput("user_parameters_cin"),
uiOutput("user_parameters_cin_2"),
uiOutput("user_parameters_skip_reseg"),
uiOutput("user_parameters_cin_3")
),
uiOutput("anal_run_cin")
),#tabName="user_param_cin"
########Tab RESULTS CIN#######
tabItem(tabName="results_cin",
HTML("<h3><i class='fa fa-star' style='color:orange'></i>   RE-SEG & SCORE</h3>"),
br(),
tabsetPanel(id="tab",
#Plots
tabPanel("Re-segmentation",
br(),
br(),
HTML("<h4 style='text-align:center'><b>Download re-segmented samples file:</b></h4>"),
div(style="text-align:center", downloadButton("ann_segments_all", label="TSV")),
div(style="text-align:center", uiOutput("samples_down_in_re_seg")),
br(),
br(),
br(),
#INDIVIDUAL PLOT:
HTML("<h4 style='text-align:center'><b>Individual segments plots</b></h4>"),
HTML("<h5 style='text-align:center'>(<i style=color:black>before</i> / <i style=color:green>after</i> re-segmentation)</h5>"),
uiOutput("choose_sample_to_plot"),
plotOutput("bef_before", height = "250px"),
plotOutput("bef_after", height = "250px"),
uiOutput("dw_buttons_plots_indv_segs"),
br(),
br(),
br(),
#Freq CN plots:
HTML("<h4 style='text-align:center'><b>Recurrent CNAs & frequency plot</b></h4>"),
div(style="text-align:center", uiOutput("cnfreq_options")),
fluidRow(
column(2),
column(4,
uiOutput("sub_variable")
),
column(4,
uiOutput("sub_sub_variable")
),
column(2)
),
uiOutput("cnfreq_plot_button"),
br(),
uiOutput("few_samples"),
plotlyOutput("freq_cn_filt"),
uiOutput("dw_button_cnfreq"),
br(),
br()
),
tabPanel("CNA Scores",value="scores",
br(),
br(),
#Boxplot CNA Scores:
HTML("<h4 style='text-align:center'><b>CNA Scores distribution</b></h4>"),
div(style="text-align:center", uiOutput("box_scores_options")),
fluidRow(
column(2),
column(4,
uiOutput("sub_variable_score")
),
column(4,
uiOutput("sub_sub_variable_score")
),
column(2)
),
uiOutput("score_plot_button"),
br(),
# uiOutput("few_samples"),
# fluidRow(
# column(4,
# plotOutput("box_BCS", height="300px")
# # uiOutput("dw_button_BCS")
# ),
# column(4,
# plotOutput("box_FCS", height="300px")
# ),
# column(4,
# plotOutput("box_GCS", height="300px")
# )
# ),
fluidRow(
column(2),
column(8,
plotOutput("box_BCS"),
uiOutput("dw_button_BCS_plot")
),
column(2)
),
br(),
fluidRow(
column(2),
column(8,
plotOutput("box_FCS"),
uiOutput("dw_button_FCS_plot")
),
column(2)
),
br(),
fluidRow(
column(2),
column(8,
plotOutput("box_GCS"),
uiOutput("dw_button_GCS_plot")
),
column(2)
),
br(),
br(),
br(),
HTML("<h4 style='text-align:center'><b>CNA Scores and annotations by samples</b></h4>"),
br(),
fluidRow(
column(11,
dataTableOutput("scores"),
div(style="text-align:right", downloadButton("download_scores",label="TSV"))
)
),
br(),
# br(),
# br(),
#
#
#
#
# HTML("<h4 style='text-align:center'><b>Hierarchical clustering for sample CNA Scores</b></h4>"),
# uiOutput("ht_scores_plot_button"),
# br(),
# plotlyOutput("heatmap_scores",width="100%", height="600px"),
# uiOutput("dw_buttons_ht_scores"),
#
# br(),
br()
# downloadButton("download_scores_raw",label="Download scores (raw)")
),
tabPanel("Variable association",value="clinical",
br(),
HTML("<h4><b>Parametric tests</b> <i>(p-values)</i></h4>"),
dataTableOutput("pval.parametric"),
div(style="text-align:right", downloadButton("download_pval.parametric",label="TSV")),
br(),
br(),
br(),
HTML("<h4><b>Non-parametric tests</b> <i>(p-values)</i></h4>"),
dataTableOutput("pval.nonparametric"),
div(style="text-align:right", downloadButton("download_pval.nonparametric",label="TSV")),
br(),
br()
),
tabPanel("Survival analysis",value="clinical",
br(),
HTML("<h4><b>Survival analysis</b> <i>(by annotation variables)</i></h4>"),
br(),
HTML("<h5>Choose your variables:</h5>"),
br(),
div(style="text-align:center", uiOutput("prepare_surv_analysis")),
uiOutput("sub_g_var"),
uiOutput("not_enough_groups_surv"),
br(),
uiOutput("button_run_surv"),
br(),
fluidRow(
column(2),
column(8,
# uiOutput("message"),
plotOutput("surv_curves_plot"),
uiOutput("dw_button_survival_plot")
),
column(2)
),
br(),
br(),
br()
)
# tabPanel("Predictions",value="predict",
# downloadButton("download_predictions",label="Download predictions"),
# dataTableOutput("predictions.tab")
# )
)
),#tabName="results_cin"
########Tab PARAM PROFILING#######
tabItem(tabName="user_param_seg",
HTML("<h3><i class='fa fa-map' style='color:orange'></i>   REGION PROFILE</h3>"),
br(),
# User analasys parameters panel
div(id="USER_PARAM",
div(style="text-align:right;", uiOutput("help_param")),
uiOutput("user_parameters"),
br(),
uiOutput("user_parameters_2"),
uiOutput("user_parameters_3")
),
uiOutput("anal_run")
),#tabName="user_param_seg"
########Tab RESULTS PROFILING#########
tabItem(tabName="seg_cna_profile_tab",
HTML("<h3><i class='fa fa-map' style='color:orange'></i>   REGION PROFILE</h3>"),
br(),
uiOutput("cn_profiling_TITLE"),
sidebarLayout(position="right",
sidebarPanel(width=3,
uiOutput("user_friendly_plot_param_1"),
uiOutput("user_friendly_plot_param_2"),
uiOutput("user_friendly_plot_param_3"),
uiOutput("message_text")
),
mainPanel(width=9,
tabsetPanel(
tabPanel(title="CNA region profiles",
div(style="text-align:center", htmlOutput("cna_profile_heatmap_MAIN")),
br(),
plotlyOutput("cna_profile_heatmap", height="800px"),
fluidRow(
column(6,
uiOutput("dw_annotation_tracks_tab1")
),
column(6,
uiOutput("dw_buttons_cna_profile_htmp")
)
),
# br(),
# br(),
#
# uiOutput("cor_test_annot_reg"),
br(),
br(),
br(),
div(style="text-align:center", htmlOutput("cna_profile_dendro_MAIN")),
uiOutput("cna_prof_dendro_plot_button"),
# uiOutput("prova_1"),
# uiOutput("prova_2"),
# uiOutput("prova_3"),
# uiOutput("prova_4"),
br(),
# uiOutput("dendro_type_box"),
plotlyOutput("cna_profile_dendrogram", height="700px", width = "100%"),
uiOutput("dw_buttons_dendro_profile"),
br(),
br(),
br(),
uiOutput("tab_genes_MAIN"),
uiOutput("select_reg_genes"),
dataTableOutput("tab_genes_reg"),
uiOutput("dw_tab_genes_bttn"),
br(),
br()
),
tabPanel(title="CNA region frequencies",
div(style="text-align:center", htmlOutput("cna_events_by_regs_MAIN")),
br(),
plotlyOutput("cna_events_by_regs", height="600px"),
uiOutput("dw_buttons_cna_events_by_regs"),
br(),
br(),
br(),
div(style="text-align:center", htmlOutput("cna_events_MAIN")),
br(),
plotlyOutput("cna_events", height="700px"),
fluidRow(
column(6,
uiOutput("dw_annotation_tracks_tab3")
),
column(6,
uiOutput("dw_buttons_cna_events_barplot")
)
),
br(),
br()
),
tabPanel(title="Correlation profiles",
div(style="text-align:center", htmlOutput("unsupervised_corr_heatmap_MAIN")),
br(),
plotlyOutput("unsupervised_corr_sample_heatmap", height = "700px"),
fluidRow(
column(6,
uiOutput("dw_annotation_tracks_tab2")
),
column(6,
uiOutput("dw_buttons_unsup_corr_htmp")
)
),
br(),
br(),
br(),
div(style="text-align:center", htmlOutput("cor_samples_dendro_MAIN")),
uiOutput("dendro_type_box_cor_plot_button"),
br(),
uiOutput("dendro_type_box_cor"),
plotlyOutput("cor_samples_dendrogram", height="700px", width="100%"),
uiOutput("dw_buttons_dendro_cor"),
br(),
br()
)
)
)
)
),#tabName="corr_tab"
#######Tab LIMMA#######
tabItem(tabName="limma_tab",
HTML("<h3><i class='fa fa-map' style='color:orange'></i>   REGION PROFILE</h3>"),
br(),
uiOutput("descriptive_regions_TITLE"),
sidebarLayout(position="right",
sidebarPanel(width=3,
uiOutput("side_param_limma"),
uiOutput("side_param_limma_2"),
uiOutput("signif"),
uiOutput("text_limma")
),
mainPanel(width=9,
tabsetPanel(
tabPanel(title="Student's t-test",
div(style="text-align:center", htmlOutput("limma_heatmap_MAIN")),
withTags(i(uiOutput("not_differences_2"))),
plotlyOutput("limma_heatmap", height="900px"),
uiOutput("dw_buttons_limma_heatmap"),
div(style="text-align:center", htmlOutput("reg_boxplot_MAIN")),
#withTags(i(uiOutput("not_differences"))),
plotOutput("reg_boxplot", height="500px"),
uiOutput("dw_buttons_reg_boxplot"),
br(),
div(style="text-align:left", htmlOutput("t_genes_reg_MAIN")),
dataTableOutput("t_genes_reg"),
uiOutput("dw_tab_genes_in_reg"),
br(),
br()
),
tabPanel(title="Fisher's test",
div(style="text-align:center", htmlOutput("fisher_heatmap_MAIN")),
withTags(i(uiOutput("not_differences_2_fisher"))),
plotlyOutput("fisher_heatmap", height="900px"),
uiOutput("dw_buttons_fisher_heatmap"),
div(style="text-align:center", htmlOutput("reg_stacked_MAIN")),
#withTags(i(uiOutput("not_differences_fisher"))),
plotlyOutput("reg_stacked", height="500px"),
uiOutput("dw_buttons_reg_stacked"),
br(),
div(style="text-align:left", htmlOutput("t_genes_reg_MAIN_fisher")),
dataTableOutput("t_genes_reg_fisher"),
uiOutput("dw_tab_genes_in_reg_fisher"),
br(),
br()
)
)
)
)
),#tabName="limma_tab"
# ########Tab HOME MODEL#########
# tabItem(tabName="home_model",
# div(tags$h3("User classifier model ", tags$i("( by Random Forest)"))),
#
# div(id="home_model",
# div(style="text-align:right;", uiOutput("help_home_model")),
# uiOutput("home_model")
# )
#
# ),#tabName="home_model"
#########Tab CREATE MODEL PARAM#########
tabItem(tabName="tab_create_param",
HTML("<h3><i class='fa fa-microchip' style='color:orange'></i>   CLASSIFIER MODEL</h3>"),
br(),
fluidRow(
column(10,
HTML("<h4>Generate your classifier model <i>(by Random Forest)</i></h4>")
),
column(2,
div(style="text-align:right;", actionLink("helpparam_machine","Help", icon=icon("question-circle-o"))),
bsModal("modal_param_machine","HELP: User parameters CLASSIFIER MODEL","helpparam_machine", includeHTML("./aux_files/help_with_param_model.html"))
)
),
br(),
uiOutput("run_parts_in_create_model_cin"),
uiOutput("run_parts_in_create_model_profile"),
uiOutput("run_parts_in_create_model_data_loaded"),
# br(),
# tableOutput("global_df"),
br(),
br(),
br(),
uiOutput("create_model_param"),
# uiOutput("subselect_groups_model"),
uiOutput("create_model_param_2"),
uiOutput("error_model"),
# br(),
# uiOutput("classy_vars"),
# tableOutput("global_df_2"),
#uiOutput("jjjj"),
br(),
br(),
br(),
hidden(div(id="div_results_model",
uiOutput("model_results_MAIN"),
br(),
wellPanel(
uiOutput("vars_in_model")),
# verbatimTextOutput("summary_data_model"),
br(),
fluidRow(
column(4,
div(style="text-align:left", wellPanel(uiOutput("model_accuracy")))
# br(),
# div(style="text-align:left", wellPanel(plotlyOutput("acc_bar", inline = FALSE)))
)
),
br(),
wellPanel(
uiOutput("final_stats_model_MAIN"),
div(style="text-align:left", tableOutput("final_stats_model")),
br(),
div(style="text-align:left", tableOutput("n_samples_table"))
),
br(),
br(),
br(),
uiOutput("bar_plot_predictions_MAIN"),
div(style="text-align:center", wellPanel(plotlyOutput("bar_plot_predictions", width = "80%", inline = TRUE))),
br(),
br(),
br(),
uiOutput("bar_plot_real_MAIN"),
div(style="text-align:center", wellPanel(plotlyOutput("bar_plot_real", width = "80%", inline = TRUE))),
br(),
br(),
br(),
dataTableOutput("final_table_model"),
uiOutput("dw_button_freq_final"),
br(),
br()
))#div
)#tabName="model_results"
# ),#tabName="model_results"
#
# #########Tab CREATE MODEL RESULTS#########
# # tabItem(tabName="tab_create_results",
# # div(tags$h3("Generate your classifier model ", tags$i("( by Random Forest)")))
# #
# # ),#tabName="model_results"
#
#
#
# #########Tab MY MODEL PARAM#########
# tabItem(tabName="tab_my_model_param",
# HTML("<h3><i class='fa fa-microchip' style='color:orange'></i>   CLASSIFIER MODEL</h3>"),
# br(),
# HTML("<h4>User classifier model <i>(by Random Forest)</i></h4>"),
#
# br(),
# uiOutput("my_model_param"),
# br(),
#
# div(style="text-align:center",actionBttn("button_my_model", "Use my model", style="fill", size="md", color="success")),
# busyIndicator(text="Running", wait=200),
#
# br(),
# br()
#
# ),#tabName="model_results"
#
# #########Tab MY MODEL RESULTS#########
# tabItem(tabName="tab_my_model_results",
# div(tags$h3("User classifier model results", tags$i("( by Random Forest)")))
#
# )#tabName="model_results"
)#tabItems
#################
)#dashboardBody
)#dashboardPage