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server.R
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server.R
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# Server file for LocusCompare
# Boxiang Liu
# 2018-01-01
options(shiny.maxRequestSize=5*1024^2)
logs = reactiveValues(user_count = 0, conn_count = 0)
pool_info = dbGetInfo(locuscompare_pool)
message('###############')
message('# APP STARTED #')
message('###############')
#############
# Functions #
#############
select_snp = function(click,merged){
merged_subset = nearPoints(merged,click,maxpoints=1,threshold = 10)
snp = merged_subset %>% dplyr::select(rsid) %>% unlist()
return(snp)
}
select_row = function(click,x){
subset = nearPoints(x, click, maxpoints = 1)
return(subset)
}
get_trait=function(study, conn = locuscompare_pool){
if (study==''){
trait = ''
} else if (str_detect(study,'^GWAS_')){
trait = dbGetQuery(
conn = conn,
statement = sprintf(
"select display_trait
from %s_trait;",study)
)
} else if (str_detect(study,'QTL_')){
trait = dbGetQuery(
conn = conn,
statement = sprintf(
"select gene_name
from %s_trait;",study)
)
} else {
trait = ''
}
trait = unname(unlist(trait))
return(trait)
}
get_study = function(selected_published,study,trait,datapath,coordinate,genome){
conn = do.call(dbConnect, args)
on.exit(dbDisconnect(conn))
if (str_detect(study,'^eQTL')){
if (str_detect(trait,'ENSG')){
res = trait
} else {
res = dbGetQuery(
conn = conn,
statement = sprintf(
"select gene_id
from gencode_v19_gtex_v6p
where gene_name = '%s'",
trait
)
)
trait = res$gene_id[1]
}
}
if (str_detect(study,'^GWAS')){
res = dbGetQuery(
conn = conn,
statement = sprintf(
"select trait
from %s_trait
where display_trait = '%s'",
study,
trait
)
)
trait = res$trait[1]
}
if (selected_published){
res=dbGetQuery(
conn = conn,
statement = sprintf(
"select t1.rsid, t1.pval
from %s as t1
join %s as t2
on t1.rsid = t2.rsid
where t1.trait = '%s'
and t2.chr = '%s'
and t2.pos >= %s
and t2.pos <= %s;",
study,
genome,
trait,
coordinate$chr,
coordinate$start,
coordinate$end
)
)
} else {
res=fread(datapath,header=TRUE,colClasses=c(rsid='character',pval='numeric'))
shiny::validate(need(all(c('rsid','pval')%in%colnames(res)),'Input file must have columns rsid, pval!'))
rsid_list=dbGetQuery(
conn = conn,
statement = sprintf(
"select rsid
from %s
where chr = '%s'
and pos >= %s
and pos <= %s;",
genome,
coordinate$chr,
coordinate$start,
coordinate$end
)
)
res = res %>% dplyr::filter(rsid %in% rsid_list$rsid)
}
setDT(res)
return(res)
}
preview_eCAVIAR = function(gwas, trait, conn = locuscompare_pool){
statement = sprintf(
"select eqtl, gene_name, clpp
from eCAVIAR
where gwas = '%s'
and trait = '%s'",
gwas,
trait
)
eCAVIAR_preview = dbGetQuery(
conn = conn,
statement = statement
)
setDT(eCAVIAR_preview)
setorder(eCAVIAR_preview, -clpp)
eCAVIAR_preview_2 = eCAVIAR_preview[,list(Tested = .N, Genes = paste(gene_name, collapse = ',')), by = 'eqtl']
setnames(eCAVIAR_preview_2,'eqtl','eQTL')
return(eCAVIAR_preview_2)
}
get_eCAVIAR = function(gwas, trait, eqtl, conn = locuscompare_pool){
statement = sprintf(
"select *
from eCAVIAR
where gwas = '%s'
and trait = '%s'
and eqtl = '%s'",
gwas,
trait,
eqtl
)
eCAVIAR = dbGetQuery(
conn = conn,
statement = statement
)
setDT(eCAVIAR)
setnames(eCAVIAR,'chr','chrom')
if (!str_detect(eCAVIAR$chrom[1],'chr')){
eCAVIAR[,chrom := paste0('chr',chrom)]
}
return(eCAVIAR)
}
epochTime = function() {
as.integer(Sys.time())
}
humanTime = function() {
format(Sys.time(), "%Y%m%d-%H%M%OS")
}
saveData = function(data,dir,name) {
fileName = sprintf("%s_%s_info.csv",
name,
humanTime())
write.csv(x = data, file = file.path(dir, fileName),
row.names = FALSE, quote = FALSE)
}
fwrite_return = function(x,file,sep){
fwrite(x=x,file=file,sep=sep)
return(file)
}
ggsave_return = function(filename,plot,width,height){
ggsave(filename=filename,plot=plot,width=width,height=height)
return(filename)
}
get_coloc_trait = function(gwas, conn = locuscompare_pool){
statement = sprintf("select distinct trait from eCAVIAR where gwas = '%s';", gwas)
result = dbGetQuery(
conn = conn,
statement = statement
)
return(result$trait)
}
get_coloc_eqtl = function(gwas, trait, conn = locuscompare_pool){
statement = sprintf("select distinct eqtl from eCAVIAR where gwas = '%s' and trait = '%s';", gwas, trait)
result = dbGetQuery(
conn = conn,
statement = statement
)
return(result$eqtl)
}
shinyServer(function(input, output, session) {
message('SESSION STARTED.')
# observe({
# input$preview_coloc
# input$plot_coloc
# input$coloc_to_locuscompare
# input$interactive_to_locuscompare
# message('Number of free connections:', pool_info$numberFreeObjects)
# message('Number of taken connections:', pool_info$numberTakenObjects)
# })
onSessionStart = isolate({
logs$user_count = logs$user_count + 1
message('Number of users: ',logs$user_count)
})
onSessionEnded(function(){
isolate({
logs$user_count = logs$user_count - 1
message('SESSION ENDED.')
message('Number of users: ',logs$user_count)
})
})
#----------------------------#
# Session-specific variables #
#----------------------------#
tmp_dir = paste0(tempdir(),'/',session$token,'/')
dir.create(tmp_dir,recursive = TRUE)
Sys.chmod(tmp_dir, mode="0777")
observeEvent(input$go_to_website,{
hide(id = "select-genome", anim = TRUE, animType = "fade")
show(id = "app-content")
})
genome = reactive({
if (input$genome_assembly == 'GRCh37/hg19') {
return('tkg_p3v5a_hg19')
} else {
return('tkg_p3v5a_hg38')
}
})
transcriptome = reactive({
if (input$genome_assembly == 'GRCh37/hg19') {
return('gencode_v19_gtex_v6p')
} else {
return('gencode_v19_gtex_v6p_hg38')
}
})
#--------------------#
# Interactive mode #
#--------------------#
observeEvent(input$study1,{
trait1=get_trait(input$study1)
updateSelectizeInput(session, "trait1", choices = trait1, server = TRUE)
})
observeEvent(input$study2,{
trait2=get_trait(input$study2)
updateSelectizeInput(session, "trait2", choices = trait2, server = TRUE)
})
selected_published_1 = reactive({isTruthy(input$study1) & isTruthy(input$trait1)})
selected_published_2 = reactive({isTruthy(input$study2) & isTruthy(input$trait2)})
study1_total = reactive({
uploaded_new = isTruthy(input$file1) & isTruthy(input$file1_trait)
return(selected_published_1() + uploaded_new)
})
output$check_study1 = renderText({
if (study1_total() == 0){
return('Please either select or upload Study 1.')
} else if (study1_total() == 1){
return('Study 1 has a valid input.')
} else if (study1_total() == 2){
return('Please either select or upload a study, but not both.')
} else {
return('Please contact Boxiang Liu at jollier.liu@gmail.com')
}
})
study2_total = reactive({
uploaded_new = isTruthy(input$file2) & isTruthy(input$file2_trait)
return(selected_published_2() + uploaded_new)
})
output$check_study2 = renderText({
if (study2_total() == 0){
return('Please either select or upload Study 2.')
} else if (study2_total() == 1){
return('Study 2 has a valid input.')
} else if (study2_total() == 2){
return('Please either select or upload a study, but not both.')
} else {
return('Please contact Boxiang Liu at jollier.liu@gmail.com')
}
})
selected_snp_region = reactive({isTruthy(input$reference_snp) & isTruthy(input$snp_window)})
selected_gene_region = reactive({isTruthy(input$reference_gene) & isTruthy(input$gene_window)})
selected_coordinate = reactive({isTruthy(input$chr) & isTruthy(input$start) & isTruthy(input$end)})
region_total = reactive({
return(selected_snp_region() + selected_gene_region() + selected_coordinate())
})
output$check_region = renderText({
if (region_total() == 0){
return('Please either type in a SNP, a gene, or a coordinate.')
} else if (region_total() == 1){
return('Region has a valid input.')
} else if (region_total() > 1){
return('Please select only one of SNP, gene, or coordinate.')
} else {
return('Please contact Boxiang Liu at jollier.liu@gmail.com')
}
})
interactive_to_locuscompare_ready = reactive({
study1_total() == 1 & study2_total() == 1 & region_total() == 1
})
coloc_to_locuscompare_ready = reactive({
isTruthy(input$coloc_gwas) & isTruthy(input$coloc_trait) & isTruthy(input$coloc_eqtl)
})
either_to_locuscompare_ready = reactive({
message(sprintf('Interactive ready? %s',interactive_to_locuscompare_ready()))
message(sprintf('Colocalization ready? %s',coloc_to_locuscompare_ready()))
interactive_to_locuscompare_ready() || coloc_to_locuscompare_ready()
})
observe({
shinyjs::toggleState('interactive_to_locuscompare', interactive_to_locuscompare_ready())
})
counter = reactiveVal(list(count = 0, from = ''))
observeEvent(
eventExpr = {input$interactive_to_locuscompare},
handlerExpr = {
new_count = counter()[['count']] + 1
new_from = 'interactive_to_locuscompare'
counter(list(count = new_count, from = new_from))
}
)
observeEvent(
eventExpr = {input$coloc_to_locuscompare},
handlerExpr = {
new_count = counter()[['count']] + 1
new_from = 'coloc_to_locuscompare'
counter(list(count = new_count, from = new_from))
message(sprintf('Click count: %s',new_count))
message(sprintf('Click from: %s',new_from))
}
)
observeEvent(counter(), {
if (interactive_to_locuscompare_ready()){
message('Interactive -> LocusCompare')
showTab(inputId = "navbarPage", target = "Plots", select = TRUE)
}
if (coloc_to_locuscompare_ready()){
shiny::req(coloc_gene_id())
message('Colocalization -> LocusCompare')
showTab(inputId = "navbarPage", target = "Plots", select = TRUE)
}
})
observeEvent(input$back,{
if (counter()[['from']] == 'interactive_to_locuscompare'){
message('Back to Interactive')
showTab(inputId = 'navbarPage', target = 'Single Locus', select = TRUE)
} else if (counter()[['from']] == 'coloc_to_locuscompare'){
message('Back to Colocalization')
showTab(inputId = 'navbarPage', target = 'Colocalization', select = TRUE)
}
hideTab(inputId = "navbarPage", target = "Plots")
shinyjs::reset('Plots')
})
coordinate = eventReactive(counter(),{
if (counter()[['from']] == 'interactive_to_locuscompare'){
message('Interactive -> Retrieving coordinates')
if (selected_snp_region()){
chr_pos=dbGetQuery(
conn = locuscompare_pool,
statement = sprintf('select chr,pos from %s where rsid = "%s" limit 1;',genome(),input$reference_snp)
)
shiny::validate(need(nrow(chr_pos)!=0,sprintf('SNP %s not found!',input$reference_snp)))
shiny::validate(need(nrow(chr_pos)==1,sprintf('SNP %s is not unique!',input$reference_snp)))
snp_window = min(input$snp_window, 1000) # max window size = 1000kb
snp_window = max(snp_window, 1) # min window size = 1kb
res=list(
chr = chr_pos$chr,
start = chr_pos$pos - snp_window*500,
end = chr_pos$pos + snp_window*500
)
} else if (selected_gene_region()){
chr_start_end=dbGetQuery(
conn = locuscompare_pool,
statement = sprintf('select chr,start,end from %s where gene_name = "%s" limit 1;', transcriptome(), input$reference_gene)
)
shiny::validate(need(nrow(chr_start_end)!=0,sprintf('Gene %s not found!',input$reference_gene)))
shiny::validate(need(nrow(chr_start_end)==1,sprintf('Gene %s is not unique!',input$reference_gene)))
gene_window = min(input$gene_window, 1000) # max window size = 1000kb
gene_window = max(gene_window, 1) # min window size = 1kb
res=list(
chr = chr_start_end$chr,
start = chr_start_end$start - gene_window*500,
end = chr_start_end$start + gene_window*500
)
} else if (selected_coordinate()){
start_ = max(1, input$start) # min start position is 1
end_ = min(input$end, start_ + 1e6) # max end position is start + 2e6
end_ = max(start_, end_) # min end position is start
res=list(
chr = input$chr,
start = start_,
end = end_
)
} else {
res = NULL
}
} else if (counter()[['from']] == 'coloc_to_locuscompare'){
message('Colocalization -> Retrieving coordinates')
shiny::validate(need(coloc_gene_id(), label = 'coloc_gene_id'))
statement = sprintf('select chr,start,end from %s where gene_id = "%s";',transcriptome(), coloc_gene_id())
chr_start_end = dbGetQuery(
conn = locuscompare_pool,
statement = statement
)
res = list(
chr = chr_start_end$chr,
start = chr_start_end$start - 1e5,
end = chr_start_end$start + 1e5
)
} else {
shiny::req(FALSE)
}
return(res)
})
d1 = eventReactive(counter(),{
shiny::req(either_to_locuscompare_ready())
message('Getting study 1')
if (counter()[['from']] == 'interactive_to_locuscompare'){
selected_published_1_ = selected_published_1()
input_study1_ = input$study1
input_trait1_ = input$trait1
input_file1_datapath_ = input$file1$datapath
} else if (counter()[['from']] == 'coloc_to_locuscompare'){
shiny::req(coloc_gene_id())
selected_published_1_ = TRUE
input_study1_ = input$coloc_gwas
input_trait1_ = input$coloc_trait
input_file1_datapath_ = ''
} else {
shiny::req(FALSE)
}
get_study(selected_published_1_,input_study1_,input_trait1_,input_file1_datapath_,coordinate(),genome())
})
d2 = eventReactive(counter(),{
shiny::req(either_to_locuscompare_ready())
message('Getting study 2')
if (counter()[['from']] == 'interactive_to_locuscompare'){
selected_published_2_ = selected_published_2()
input_study2_ = input$study2
input_trait2_ = input$trait2
input_file2_datapath_ = input$file2$datapath
} else if (counter()[['from']] == 'coloc_to_locuscompare'){
shiny::req(coloc_gene_id())
selected_published_2_ = TRUE
input_study2_ = input$coloc_eqtl
input_trait2_ = coloc_gene_id()
input_file2_datapath_ = ''
} else {
shiny::req(FALSE)
}
get_study(selected_published_2_,input_study2_,input_trait2_,input_file2_datapath_,coordinate(),genome())
})
merged = reactive({
shiny::req(either_to_locuscompare_ready())
message('Merging studies')
d1_non_empty = d1() %>% nrow() %>% `>`(0)
d2_non_empty = d2() %>% nrow() %>% `>`(0)
shiny::validate(need(d1_non_empty,'No SNP was found in specified region for study 1. Did you specify a correct region?'))
shiny::validate(need(d1_non_empty,'No SNP was found in specified region for study 2. Did you specify a correct region?'))
merged = merge(d1(),d2(),by='rsid',suffixes=c('1','2'),all=FALSE)
merged = merged %>% get_position(.,genome())
check_overlap = merged %>% nrow() %>% `>`(0)
shiny::validate(need(check_overlap,'No overlapping SNPs between two studies'))
merged = merged %>% setDT()
merged = merged %>% mutate(logp1 = -log10(pval1),logp2 = -log10(pval2))
message('Finished merging')
return(merged)
})
snp=reactiveVal(value='',label='snp')
observeEvent(merged(),{
message('Populating SNP field')
merged() %>%
select(rsid) %>%
unname () %>%
unlist() %>%
updateSelectizeInput(session, "snp", choices = ., server = TRUE)
})
observeEvent(counter(),{
shiny::req(either_to_locuscompare_ready())
non_empty_merge = merged() %>% nrow() %>% `>`(0)
non_empty_merge %>% (
function(non_empty_merge){
if (non_empty_merge){
message('Update selected SNP')
merged() %>%
dplyr::slice(which.min(pval1*pval2)) %>%
dplyr::select(rsid) %>%
unlist() %>%
snp()
} else {
snp('')
}
}
)
})
observeEvent(input$snp,{
message('Updating selected SNP')
snp(input$snp)
})
chr=reactive({
message('Updating chromosome')
chr=unique(coordinate()$chr)
shiny::validate(need(length(chr)==1,'Studies must only have one chromosome!'))
return(chr)
})
ld=reactive({
message('Updating LD')
retrieve_LD(chr(),snp(),input$population)
})
color=reactive({
message('Updating color')
merged() %>%
dplyr::select(rsid) %>%
unlist() %>% unname() %>%
assign_color(snp(),ld())
})
shape=reactive({
message('Updating shape')
merged() %>% assign_shape(snp())
})
size=reactive({
message('Updating size')
merged() %>% assign_size(snp())
})
observeEvent(input$plot_click,{
selected_snp = merged() %>% select_snp(input$plot_click,.)
nonempty_snp = selected_snp %>% identical(character(0)) %>% `!`
if (nonempty_snp){
selected_snp %>% snp()
}
})
range=reactiveValues(xmin=NULL,xmax=NULL)
observeEvent(input$plot_dblclick,{
brush = input$plot_brush
if (!is.null(brush)) {
range$xmin = brush$xmin
range$xmax = brush$xmax
} else {
range$xmin=NULL
range$xmax=NULL
}
})
plot_data=reactive({
message('Making plot_data')
if (is.null(range$xmin)){
plot_data = merged()
} else {
plot_data = merged() %>% dplyr::filter(pos<=range$xmax,pos>=range$xmin)
}
plot_data = plot_data %>% mutate(label=ifelse(rsid==snp(),rsid,''))
return(plot_data)
message('Finished making plot_data')
})
title1=reactive({
if (counter()[['from']] == 'interactive_to_locuscompare'){
if (isTruthy(input$trait1)){
return(input$trait1)
} else {
return(input$file1_trait)
}
} else if (counter()[['from']] == 'coloc_to_locuscompare'){
return(input$coloc_trait)
} else {
shiny::req(FALSE)
}
})
title2=reactive({
if (counter()[['from']] == 'interactive_to_locuscompare'){
if (isTruthy(input$trait2)){
return(input$trait2)
} else {
return(input$file2_trait)
}
} else if (counter()[['from']] == 'coloc_to_locuscompare'){
return(coloc_gene_id())
} else {
shiny::req(FALSE)
}
})
msg = reactive({
sprintf('%s and %s has no overlapping SNP in %s:%s-%s!',
title1(),
title2(),
coordinate()$chr,
coordinate()$start,
coordinate()$end
)
})
output$locuscompare = renderPlot({
nonempty = plot_data() %>% nrow() %>% `>`(0)
shiny::validate(need(nonempty,msg()))
message('Making LocusCompare plot')
p = make_locuscatter(
merged = plot_data(),
title1 = title1(),
title2 = title2(),
ld = ld(),
color = color(),
shape = shape(),
size = size(),
legend=FALSE
)
return(p)
})
output$locuszoom1 = renderPlot({
nonempty = plot_data() %>% nrow() %>% `>`(0)
shiny::validate(need(nonempty,msg()))
message('Making locuszoom plot 1')
p = make_locuszoom(
metal = plot_data(),
title = title1(),
ld = ld(),
color = color(),
shape = shape(),
size = size(),
y_string='logp1'
)
return(p)
})
output$locuszoom2 = renderPlot({
nonempty = plot_data() %>% nrow() %>% `>`(0)
shiny::validate(need(nonempty,msg()))
message('Making locuszoom plot 2')
p = make_locuszoom(
metal = plot_data(),
title = title2(),
ld = ld(),
color = color(),
shape = shape(),
size = size(),
y_string='logp2'
)
return(p)
})
output$blank_plot = renderPlot({
p = plot_data() %>% {ggplot() + geom_blank()}
return(p)
})
output$snp_info = renderText({
res = dbGetQuery(
conn = locuscompare_pool,
statement = sprintf('select * from %s where rsid = "%s";',genome(),snp()))
sprintf(
'Chromosome: %s\nPosition: %s\nrs ID: %s\nReference SNP: %s\nAlternate SNP: %s\nAllele Frequency: %s\nAFR Frequency: %s\nAMR Frequency: %s\nEAS Frequency: %s\nEUR Frequency: %s\nSAS Frequency: %s',
res$chr,
res$pos,
res$rsid,
res$ref,
res$alt,
res$AF,
res$AFR_AF,
res$AMR_AF,
res$EAS_AF,
res$EUR_AF,
res$SAS_AF
)
})
output$ld_snps = renderDataTable({
shiny::req(coordinate())
ld_snps=ld() %>%
dplyr::filter(SNP_A==snp()) %>%
dplyr::select(rsid=SNP_B,r2=R2)
ld_snps=rbind(data.frame(rsid=snp(),r2=1),ld_snps)
ld_snps_2 = merged() %>%
dplyr::mutate(pval1_disp = format.pval(pval1), pval2_disp = format.pval(pval2)) %>%
dplyr::select(rsid,chr,pos,pval1_disp,pval2_disp) %>%
merge(ld_snps,by='rsid') %>%
dplyr::rename(rsID = rsid, Chromosome = chr, Position = pos, `P-value (x-axis)` = pval1_disp, `P-value (y-axis)` = pval2_disp, `LD (r2)` = r2) %>%
datatable(., selection='none')
return(ld_snps_2)
})
output$file1_example = downloadHandler(
filename = function(){return('PHACTR1_Artery_Coronary.tsv')},
content = function(file){file.copy(sprintf('%s/data/example/PHACTR1_Artery_Coronary.tsv',home_dir),file)},
contentType = 'text/txt')
output$file2_example = downloadHandler(
filename = function(){return('PHACTR1_Coronary_Heart_Disease_Nikpay_2015.tsv')},
content = function(file){file.copy(sprintf('%s/data/example/PHACTR1_Coronary_Heart_Disease_Nikpay_2015.tsv',home_dir),file)},
contentType = 'text/txt')
output$single_download = downloadHandler(
filename=function(){return('results.zip')},
content=function(file){
data_fn = merged() %>% fwrite_return(paste0(tmp_dir,'/data.tsv'),sep='\t')
fwrite(ld(),paste0(tmp_dir,'/ld.tsv'),sep='\t')
locuscompare = make_locuscatter(
merged = plot_data(),
title1 = title1(),
title2 = title2(),
ld = ld(),
color = color(),
shape = shape(),
size = size(),
legend=FALSE)
locuszoom1 = make_locuszoom(
metal = plot_data(),
title = title1(),
ld = ld(),
color = color(),
shape = shape(),
size = size(),
y_string='logp1')
locuszoom2 = make_locuszoom(
metal = plot_data(),
title = title2(),
ld = ld(),
color = color(),
shape = shape(),
size = size(),
y_string='logp2')
length_ = input$locuscompare_length
width_ = input$locuszoom_width
height_ = input$locuszoom_height
locuscompare_fn = locuscompare %>% ggsave_return(paste0(tmp_dir,'/locuscompare.pdf'),.,width=length_,height=length_)
locuszoom1_fn = locuszoom1 %>% ggsave_return(paste0(tmp_dir,'/locuszoom1.pdf'),.,width=width_,height=height_)
locuszoom2_fn = locuszoom2 %>% ggsave_return(paste0(tmp_dir,'/locuszoom2.pdf'),.,width=width_,height=height_)
c(data_fn,paste0(tmp_dir,'/ld.tsv'),locuscompare_fn,locuszoom1_fn,locuszoom2_fn) %>% utils::zip(file,.,flags = '-j')
}
)
#----------------#
# Colocalization #
#----------------#
observeEvent(
eventExpr = input$coloc_gwas,
handlerExpr = {
coloc_trait = get_coloc_trait(input$coloc_gwas)
updateSelectizeInput(session, "coloc_trait", choices = coloc_trait, server = FALSE)
}
)
observeEvent(
eventExpr = input$coloc_trait,
handlerExpr = {
coloc_eqtl = get_coloc_eqtl(input$coloc_gwas, input$coloc_trait)
updateSelectizeInput(session, "coloc_eqtl", choices = coloc_eqtl, server = FALSE)
}
)
eCAVIAR_preview = eventReactive(
eventExpr = input$preview_coloc,
valueExpr = {
preview_eCAVIAR(input$coloc_gwas, input$coloc_trait)
}
)
output$coloc_table = renderDataTable(
expr = eCAVIAR_preview() %>% datatable(.,rownames = FALSE, selection='none',options = list(scrollX = TRUE)),
)
eCAVIAR = eventReactive(
eventExpr = input$plot_coloc,
valueExpr = {
get_eCAVIAR(input$coloc_gwas, input$coloc_trait, input$coloc_eqtl)
}
)
output$coloc_text = renderText({
sprintf('[SUMMARY] %s loci passed the threshold (GWAS lead SNP p-value < 5e-8 and eQTL lead SNP p-value < 1e-6).',nrow(eCAVIAR()))
})
output$coloc_helper_text = renderText({
eCAVIAR()
'[INSTRUCTIONS]
1. Click on a point to see more;
2. Drag and double-click to zoom in;
3. Double-click again to zoom out.'
})
build = 'hg19'
color1 = 'black'
color2 = 'black'
chrom_lengths = manhattan::get_chrom_lengths(build)
xmax = manhattan::get_total_length(chrom_lengths)
x_breaks = manhattan::get_x_breaks(chrom_lengths)
color_map = c(color1,color2)
names(color_map) = c(color1,color2)
coloc_range=reactiveValues(x=NULL)
observeEvent(input$coloc_plot_dblclick, {
brush = input$coloc_plot_brush
if (!is.null(brush)) {
coloc_range$x = c(brush$xmin, brush$xmax)
} else {
coloc_range$x = NULL
}
})
coloc_plot_data = reactive({
eCAVIAR() %>%
rename(y = clpp) %>%
manhattan::add_cumulative_pos(.,build) %>%
manhattan::add_color(., color1 = color1, color2 = color2)
})
output$coloc = renderPlot({
p = coloc_plot_data() %>%
{ggplot2::ggplot(.,aes(x=cumulative_pos,y=y,color=color))+
geom_point(size=5)+
theme_classic()+
theme(axis.title = element_text(size=20),axis.text = element_text(size=15)) +
scale_x_continuous(expand=c(0.01,0),limits=c(0,xmax),breaks=x_breaks,labels=names(x_breaks),name='Chromosome')+
scale_y_continuous(name='Coloc. Prob.', limits = c(0,NA))+
scale_color_manual(values=color_map,guide='none')+
coord_cartesian(xlim = coloc_range$x)}
return(p)
})
selected_row = eventReactive(
eventExpr = input$coloc_plot_click,