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VCFui.R
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#' Build shiny UI page
#'
#' @importFrom shinyjs useShinyjs
#' @importFrom shinyWidgets useShinydashboard
#' @importFrom shiny shinyUI fluidPage navbarPage tabPanel icon includeHTML br hr navbarMenu fluidRow strong p tags
#' @importFrom shinydashboard box
#' @importFrom shinyBS bsModal
#'
#' @export
#'
VCFui <- function() {
require(DT)
require(shiny)
require(shinyBS)
require(shinyWidgets)
require(shinydashboard)
dashboardPage(
# skin = "black",
#Header -------------------------------------------------------------------------------------------------------------------------------
dashboardHeader(title ="VCF Analyse" , titleWidth = 250),
#Sider---------------------------------------------------------------------------------------------------------------------------------
dashboardSidebar(
width = 250,
sidebarMenu(
menuItem("Introduction",tabName = "introduction",icon = icon("home")),
menuItem("Data Input", icon = icon("upload"), tabName = "datainput"),
menuItem("Venn Diagram", icon = icon("chart-bar"), tabName = "venn_analyse"),
menuItem("Variants Number", icon = icon("chart-bar"), tabName = "ALL_variants"),
menuItem("SNVs Exploration", icon = icon("chart-bar"), tabName = "snp_analysis"),
menuItem("Indels Exploration", icon = icon("chart-bar"), tabName = "Indel_analysis"),
menuItem("Genome Circos Plot", icon = icon("chart-bar"), tabName = "circle"),
menuItem("Genomic Features",icon = icon("chart-bar"), tabName = "distribution"),
menuItem("Variants Relevant Genes", icon = icon("chart-bar"), tabName = "Variants_summarise"),
menuItem("Cancer Driver Genes", icon = icon("chart-bar"), tabName = "Variants_heatmap"),
menuItem("Cancer Mutational Signature", icon = icon("chart-bar"), tabName = "cancer_signature"),
menuItem("Data Annotation", icon = icon("book"), tabName = "dataAnno")
)
),
#BODY --------------------------------------------------------------------------------------------------------------------------------------------------
dashboardBody(
includeCSS(path = system.file("shiny", "www/custom.css", package = "VCFshiny")),
tags$head(tags$style(HTML('
.main-header .logo {
font-family: "Georgia", Times, "Times New Roman", serif;
font-weight: bold;
font-size: 24px;
}
'))),
### 读入数据 ---------------------------------------------------------------------------------------------------------
tabItems(
source(system.file("shiny", "modules/0.Introduction.R", package = "VCFshiny"), local = T)$value,
source(system.file("shiny", "modules/1.Upload_ui.R", package = "VCFshiny"), local = T)$value,
### 第一部分 ---------------------------------------------------------------------------------------------------------------------------------------------
source(system.file("shiny", "modules/2.Venn_ui.R", package = "VCFshiny"), local = T)$value,
source(system.file("shiny", "modules/3.summarise_barplot_ui.R", package = "VCFshiny"), local = T)$value,
source(system.file("shiny", "modules/4.SNP_Analysis_ui.R", package = "VCFshiny"), local = T)$value,
source(system.file("shiny", "modules/5.Indel_Analysis_ui.R", package = "VCFshiny"), local = T)$value,
source(system.file("shiny", "modules/6.circle_ui.R", package = "VCFshiny"), local = T)$value,
### 第二部分 --------------------------------------------------------------------------------------------------------------------------------
source(system.file("shiny", "modules/7.Distribution_ui.R", package = "VCFshiny"), local = T)$value,
source(system.file("shiny", "modules/8.VariantsGene_Summarise_ui.R", package = "VCFshiny"), local = T)$value,
source(system.file("shiny", "modules/9.VariantsGene_Heatmap_ui.R", package = "VCFshiny"), local = T)$value,
source(system.file("shiny", "modules/10.mutational_signature_ui.R", package = "VCFshiny"), local = T)$value,
source(system.file("shiny", "modules/11.Annotation_ui.R", package = "VCFshiny"), local = T)$value
)
)
)
}