global.R

options(warn = -1)
library(shiny)
library(shinyjs)
library(shinydisconnect)
library(ggplot2)
library(stringr)
library(dplyr)
library(tidyr)
library(forcats)
library(patchwork)
library(glue)
library(ggpubr)
library(writexl)
library(snpStats)
library(IRanges)
library(LDheatmap)
library(ape)
library(pegas)
library(gridExtra)
library(grid)
library(ggtree)
library(shinycssloaders)
library(shinysky)
library(shinydashboard)
library(shinyWidgets)
library(gggenes)
library(DT)
library(shinythemes)
library(NAM)
library(adegenet)
library(rmarkdown)
library(rvg)
library(officer)
library(countup)

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")
source("script/snp_distribution.R")
source("script/diversity.R")
source("script/box_format.R")
source("script/homepage.R")
source("script/geographic_map.R")
footerTagList <- list(
  tags$footer(id = "myFooter",
              shiny::includeHTML("www/md/footer.html")
  )
)

gffinfo <- readRDS("./data/Other_data/gffinfo.rds")
load("./data/Other_data/geneinfo.RData")
load("./data/Other_data/Ref.gene.anno.RData")

chromosome <- c(
  "A01", "A02", "A03", "A04", "A05", "A06", "A07", "A08", "A09", "A10",
  "C01", "C02", "C03", "C04", "C05", "C06", "C07", "C08", "C09", "Ann", "Cnn"
)
chrinfo <- read.table("./data/Other_data/chrInfo.txt", header = T, as.is = T)
snp.list <- read.table("./data/Other_data/snp.RData.lst", header = T, as.is = T)
allele.list <- read.table("./data/Other_data/allele.RData.lst", header = T, as.is = T)
all.var <- read.table("data/Other_data/all.var.txt", header = F, as.is = T)
all.var.info <- as.character(all.var$V1)
all.var.info <- c("Winter", "Semi-winter", "Spring", "Core", all.var.info)
eff_type <- c(
  "Downstream", "Intergenic", "Non_synonymous_coding", "Synonymous_coding",
  "Intragenic", "Upstream", "Intron", "Splice_site_region", "Stop_lost",
  "Stop_gained", "Synonymous_stop", "Start_lost"
)
database_type <- c("NR", "Swiss-prot", "KEGG", "eggNOG", "GO")
available_data_formats <- c("txt", "xlsx", "csv", "tsv")
available_fig_formats <- c("png", "pptx","pdf", "jpeg", "tiff", "bmp", "svg")
all.tree.info <- read.table("./data/Other_data/all.var.tree.info.txt", head = T, as.is = T, sep = "\t", row.names = 1)
sample_geographic_info <- readRDS("./data/Other_data/sample_map_info.rds")