file-text to file-alt

.Rhistory

@@ -0,0 +1,110 @@
+if (!requireNamespace("BiocManager", quietly = TRUE))
+install.packages("BiocManager")
+BiocManager::install(version = "3.14")
+devtools::install_github("tidyverse/tidyverse")
+library(shiny)
+library(shinydisconnect)
+library(ggplot2)
+library(stringr)
+library(dplyr)
+library(tidyr)
+library(forcats)
+library(patchwork)
+library(glue)
+library(ggpubr)
+library(writexl)
+library(snpStats)
+BiocManager::install("snpStats")
+library(writexl)
+library(snpStats)
+library(IRanges)
+BiocManager::install(c("IRanges","ape","LDheatmap","pegas","ggtree"))
+options(warn = -1")
+BiocManager::install("shiny")
+BiocManager::install("shinydisconnect")
+library(IRanges)
+library(LDheatmap)
+library(ape)
+library(pegas)
+library(gridExtra)
+library(grid)
+library(ggtree)
+library(shinycssloaders)
+library(shinysky)
+devtools::install_github("AnalytixWare/ShinySky")
+library(shinydashboard)
+library(shinyWidgets)
+library(gggenes)
+library(DT)
+library(shinythemes)
+library(NAM)
+library(adegenet)
+library(rmarkdown)
+library(rvg)
+library(officer)
+source("script/mod_ldheatmap.R")
+source("script/mod_snpdistribution.R")
+source("script/mod_phylogenetics.R")
+source("script/mod_diversity.R")
+source("script/mod_extraction.R")
+source("script/mod_documentation.R")
+source("script/mod_about.R")
+source("script/extractsnp.R")
+source("script/extractallele.R")
+source("script/ldheatmap.R")
+source("script/genestru.viz.R")
+source("script/chooser.R")
+source("script/readNewData.R")
+#' @param rightLabel
+#' @param leftChoices
+#' @param rightChoices
+#' @param size
+#' @param multiple
+#'
+#' @return
+#' @export
+#'
+#' @examples
+chooserInput <- function(inputId, leftLabel, rightLabel, leftChoices, rightChoices,
+size = 2, multiple = FALSE) {
+leftChoices <- lapply(leftChoices, tags$option)
+rightChoices <- lapply(rightChoices, tags$option)
+if (multiple) {
+multiple <- "multiple"
+} else {
+multiple <- NULL
+}
+tagList(
+singleton(tags$head(
+tags$script(src = "css/chooser-binding.js"),
+tags$style(
+type = "text/css",
+HTML(".chooser-container { display: inline-block; }")
+)
+)),
+div(
+id = inputId, class = "chooser",
+div(
+class = "chooser-container chooser-left-container",
+tags$select(class = "left", size = size, multiple = multiple, leftChoices, style = "width:100px;background:gray50")
+),
+div(
+class = "chooser-container chooser-center-container",
+icon("arrow-alt-circle-right", "right-arrow fa-2x"),
+tags$br(),
+icon("arrow-alt-circle-left", "left-arrow fa-2x")
+),
+div(
+class = "chooser-container chooser-right-container",
+tags$select(class = "right", size = size, multiple = multiple, rightChoices, style = "width:100px;background:gray50")
+)
+)
+)
+}
+source("script/snp_distribution.R")
+shiny::runApp()
+BiocManager::install("markdown")
+runApp()
+runApp()
+rm(list=ls())
+runApp()

app.R

@@ -1,44 +1,44 @@
-source("global.R")
-ui <- fluidPage(
-  tags$script(src="css/addhash.js"),
-  div(img(src = "img/bnasnpdb_logo.png")),
-  includeCSS("www/css/custom.css"),
-  includeCSS("www/css/footer.css"),
-  disconnectMessage(
-    text = "Your session timed out, reload the application!",
-    refresh = "Reload now",
-    background = "#f89f43",
-    colour = "white",
-    overlayColour = "grey",
-    overlayOpacity = 0.75,
-    top = 250,
-    refreshColour = "brown"
-  ),
-  navbarPage(
-    title = "",
-    windowTitle = "Welcome to BnaSNPDB",
-    theme = shinytheme("flatly"),
-    tabPanel("Home", homepage, icon = icon("home")),
-    tabPanel("LDheatmap", mod_ldheatmap_ui("ld")),
-    tabPanel("SNPdistribution", mod_snpdistribution_ui("dis")),
-    tabPanel("Phylogenetics", mod_phylogenetics_ui("tree")),
-    tabPanel("Diversity", mod_diversity_ui("diversity")),
-    tabPanel("Extraction", mod_extraction_ui("extract"), icon = icon("search")),
-    tabPanel("Documentation", mod_doc_ui("doc"), icon = icon("file-text")),
-    tabPanel("About", mod_about_ui("about"), icon = icon("info-circle")),
-    footer = footerTagList
-  )
-)
-
-server <- function(input, output, session) {
-  callModule(mod_ldheatmap_server, "ld")
-  callModule(mod_snpdistribution_server, "dis")
-  callModule(mod_phylogenetics_server, "tree")
-  callModule(mod_diversity_server, "diversity")
-  callModule(mod_extraction_server, "extract")
-  observeEvent(input$disconnect, {
-    session$close()
-  })
-}
-
-shinyApp(ui, server)
+source("global.R")
+ui <- fluidPage(
+  tags$script(src="css/addhash.js"),
+  div(img(src = "img/bnasnpdb_logo.png")),
+  includeCSS("www/css/custom.css"),
+  includeCSS("www/css/footer.css"),
+  disconnectMessage(
+    text = "Your session timed out, reload the application!",
+    refresh = "Reload now",
+    background = "#f89f43",
+    colour = "white",
+    overlayColour = "grey",
+    overlayOpacity = 0.75,
+    top = 250,
+    refreshColour = "brown"
+  ),
+  navbarPage(
+    title = "",
+    windowTitle = "Welcome to BnaSNPDB",
+    theme = shinytheme("flatly"),
+    tabPanel("Home", homepage, icon = icon("home")),
+    tabPanel("LDheatmap", mod_ldheatmap_ui("ld")),
+    tabPanel("SNPdistribution", mod_snpdistribution_ui("dis")),
+    tabPanel("Phylogenetics", mod_phylogenetics_ui("tree")),
+    tabPanel("Diversity", mod_diversity_ui("diversity")),
+    tabPanel("Extraction", mod_extraction_ui("extract"), icon = icon("search")),
+    tabPanel("Documentation", mod_doc_ui("doc"), icon = icon("file-alt")),
+    tabPanel("About", mod_about_ui("about"), icon = icon("info-circle")),
+    footer = footerTagList
+  )
+)
+
+server <- function(input, output, session) {
+  callModule(mod_ldheatmap_server, "ld")
+  callModule(mod_snpdistribution_server, "dis")
+  callModule(mod_phylogenetics_server, "tree")
+  callModule(mod_diversity_server, "diversity")
+  callModule(mod_extraction_server, "extract")
+  observeEvent(input$disconnect, {
+    session$close()
+  })
+}
+
+shinyApp(ui, server)