Global.R

options(warn=-1)

# library(IRanges)
# library(plotly)
# library(LDheatmap)
# library(chopsticks)
# library(foreach)
# library(ape)
# library(pegas)
# library(plyr)
library(dplyr)
# library(ggmap)
# library(tidyr)
# library(gridExtra)
# library(ggtree)
# library(grid)
library(snpStats)
# library(htmlwidgets)
# library(shinycssloaders)
# library(shinysky)
# library(shinyWidgets)
# library(shinythemes)
library(shinyBS)

source("fetchSnp.R")
source("ld.heatmap.R")
source("phylo.R")
source("hapNet.R")
source("hapConten.R")
source("nucDiv.R")
source("writeHap.R")
source("hapGeo.R")
source("GBrowser.R")
source("anaReg.R")
source("geneStru.R")
source("hapGeoStatic.R")
source("snpInfo.R")
source("validReg.R")
source("alleleFreq.R")

acc.info <- read.table("./data/all.acc.txt", head=T, as.is=T, sep="\t", quote="")  
load("./data/gff.msu.v7.RData")
snp.lst <- read.table("./data/snp.RData.lst", head=T, as.is=T, sep="\t")
load("./data/gene.info.RData")

source("chooser.R")
#all.acc.cho <- acc.info$ID[!is.na(acc.info$Latitude)]
all.acc.cho <- paste(acc.info$ID, acc.info$Name, acc.info$Ecotype, sep=", ")
all.acc.cho <- c("Aus", "Indica", "IndicaI", "IndicaII", "Japonica", "TeJ", 
                 "TrJ", "Or-I", "Or-II", "Or-III", all.acc.cho)

chrInfo <- read.table("./data/chrInfo.txt", head=T, as.is=T, sep="\t")

acc.tree <- read.table("./data/acc.tree.txt", 
                       head=T, as.is=T, sep="\t", row.names = 1)

footerTagList <- list(
  tags$footer(id = "myFooter",
              shiny::includeHTML("www/footer.html")
  )
)