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global.R
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library(shinydashboard)
library(shiny)
library(haploR)
library(data.table)
library(biomaRt)
library(shinycssloaders)
library(shinyWidgets)
library(jsonlite)
library(Sushi)
library(HiTC)
library(colorspace)
library(writexl)
library(dplyr)
library(ggplot2)
library(plotly)
library(ggpubr)
logger <- function(...) {
message(strftime(Sys.time(), "[%F %T %Z] "), ...)
}
# Global Data
logger("Connecting to BioMart: ensembl, hsapiens_gene_ensemble")
ensembl54 <- useEnsembl("ensembl", dataset = "hsapiens_gene_ensembl",mirror = "useast")
logger("Loading cached HiC Data")
load("data/hicData.Rdata")
logger("Loading cached TAD data in `IMR90_domain_hg19.bed`")
tad <- fread("data/IMR90_domains_hg19.bed")
colnames(tad) <- c("chr", "start_position", "end_position")
tad$chr[tad$chr == "chrX"] <- NA_character_
tad$chr <- gsub("chr", "", tad$chr)
tad$chr <- as.numeric(tad$chr)
tad <- tad[!is.na(tad$chr), ]
enableBookmarking("url")
logger("Launching app...")
# Example links
EXAMPLES <- list(
"8q24" = list(
# rs1016343,rs10505477,rs9642880,rs13281615,rs1447295,rs1562430,rs16901979,rs16902094,rs2456449,rs4242382,rs4242384,rs445114,rs6983267,rs7014346
url = '?_inputs_&oncoParameters1=null&oncoParameters2=null&oncoParameters3=null&oncoParameters4=null¶meters=["pos_hg38"%2C"r2"%2C"query_snp_rsid"]¶meters2=["%23chromosome"%2C"coordinate"%2C"hits"%2C"score_anno"]&plotColor="1"&plotEndBP=127810818&plotStartBP=126730818&pop="EUR"&resetBP=0&sidebarCollapsed=false&sidebarItemExpanded=null&snpList="rs1016343%2Crs10505477%2Crs9642880%2Crs13281615%2Crs1447295%2Crs1562430%2Crs16901979%2Crs16902094%2Crs2456449%2Crs4242382%2Crs4242384%2Crs445114%2Crs6983267%2Crs7014346"&tabs="tab1"&update1=7&updateBP=0&value=0.8',
text = "Chromosome 8q24 cancer risk loci",
tooltip = "A selection of SNPs that could be uploaded via a text file",
input_id = NULL
),
"ancestry" = list(
url = '?_inputs_&oncoParameters1=null&oncoParameters2=null&oncoParameters3=null&oncoParameters4=null¶meters=%5B%22pos_hg38%22%2C%22r2%22%2C%22query_snp_rsid%22%5D¶meters2=%5B%22%23chromosome%22%2C%22coordinate%22%2C%22hits%22%2C%22score_anno%22%5D&plotColor=%221%22&plotEndBP=100020977&plotStartBP=99020977&pop=%22EUR%22&resetBP=0&sidebarCollapsed=false&sidebarItemExpanded=null&snpList=%22rs1229984%2C%20rs3811801%22&tabs=%22tab1%22&update1=8&updateBP=0&value=0.8',
text = "Ancestry informative markers",
tooltip = "rs1229984, rs3811801",
input_id = NULL
),
"protective" = list(
url = '?_inputs_&oncoParameters1=null&oncoParameters2=null&oncoParameters3=null&oncoParameters4=null¶meters=%5B%22pos_hg38%22%2C%22r2%22%2C%22query_snp_rsid%22%5D¶meters2=%5B%22%23chromosome%22%2C%22coordinate%22%2C%22hits%22%2C%22score_anno%22%5D&plotColor=%221%22&plotEndBP=118518477&plotStartBP=117838477&pop=%22EUR%22&resetBP=0&sidebarCollapsed=false&sidebarItemExpanded=null&snpList=%22rs3754127%2C%20rs3765501%2C%20rs4658973%22&tabs=%22tab1%22&update1=47&updateBP=0&value=0.9',
text = "Potentially protective of DNA damage",
tooltip = "rs3754127, rs3765501, rs4658973",
input_id = NULL
)
)