Master locuscompare

.gitignore

@@ -14,6 +14,7 @@ data/gtex
 data/ld
 data/population
 data/qtl
+data/SMR
 .DS_Store
 ._*
 .Rproj.user
@@ -22,3 +23,4 @@ locuscompare.Rproj
 tmp/
 README.html
 .httr-oauth
+maintenance/

README.md

@@ -4,9 +4,13 @@
 LocusCompare is an interactive visualization tool for comparing two genetic association datasets. For instance, it can be used to visualize the colocalization between a GWAS dataset to an eQTL dataset, which is particularly useful for fine-mapping studies. 
 
 ## Usage
-Please see the [FAQ page](https://github.com/boxiangliu/locuscompare/wiki/1.-FAQ) and the [documentation page](https://github.com/boxiangliu/locuscompare/wiki)
+Please see the [FAQ page](https://github.com/boxiangliu/locuscompare/wiki/FAQ) and the [documentation page](https://github.com/boxiangliu/locuscompare/wiki)
 
 
 ## Questions
 For questions and bug reports, please open an issue [here](https://github.com/boxiangliu/locuscompare/issues). 
 
+## Citation
+If you use locuscompare, please cite the following paper: https://www.nature.com/articles/s41588-019-0404-0
+
+Boxiang Liu, Michael J. Gloudemans, Abhiram S. Rao, Erik Ingelsson & Stephen B. Montgomery (2019) Abundant associations with gene expression complicate GWAS follow-up, Nature Genetics

about.md

@@ -4,7 +4,7 @@
 ## Introduction
 <img src="logo.png" width="600"/>
 
-LocusCompare is a suite of tools and datasets to visualize the colocalization of summary statistics from pairs of association datasets (e.g. GWAS and eQTL). These tools and datasets inclue: 
+LocusCompare is a suite of tools and datasets to visualize the colocalization of summary statistics from pairs of association datasets (e.g. GWAS and eQTL). These tools and datasets include: 
 
 - Colocalization statistics between more than 200 GWAS and 48 GTEx (version 7) tissues
 - Interactive LocusCompare plot to visualize a single locus
@@ -13,13 +13,14 @@ LocusCompare is a suite of tools and datasets to visualize the colocalization of
 ## Documentations
 For instructions please follow these links: 
 
-- [Documentation](https://github.com/boxiangliu/locuscompare/wiki)
-- [Frequently Asked Questions](https://github.com/boxiangliu/locuscompare/wiki/FAQ)
-- [Report a bug](https://github.com/boxiangliu/locuscompare/issues)
+
+- <a href="https://www.github.com/boxiangliu/locuscompare/wiki" target="_blank">Documentation</a>
+- <a href="https://www.github.com/boxiangliu/locuscompare/wiki/FAQ" target="_blank">Frequently Asked Questions</a>
+- <a href="https://www.github.com/boxiangliu/locuscompare/issues" target="_blank">Bug reports</a>
 
 To download stand-alone version:
 
-- [LocusCompareR](https://github.com/boxiangliu/locuscomparer)
+- <a href="https://www.github.com/boxiangliu/locuscomparer" target="_blank">LocusCompareR</a>
 
 
 ## License
@@ -28,4 +29,10 @@ GPL v3 or later
 ## Developers
 - Boxiang Liu (author, maintainer)
 - Mike Gloudemans (author, maintainer)
+- Abhiram Rao (author)
 - Stephen Montgomery (author)
+
+## Citation
+If you use locuscompare, please cite the following paper: https://www.nature.com/articles/s41588-019-0404-0
+
+Boxiang Liu, Michael J. Gloudemans, Abhiram S. Rao, Erik Ingelsson & Stephen B. Montgomery (2019) Abundant associations with gene expression complicate GWAS follow-up, Nature Genetics

global.R

@@ -12,10 +12,10 @@ source('locuscompare.R')
 source('config/config.R')
 library(digest)
 library(utils)
-library(googlesheets)
+library(googlesheets4)
 library(promises)
 library(future)
-plan(multiprocess)
+plan (multisession)
 library(mailR)
 library(shinycssloaders)
 library(googledrive)

locuscompare.R

@@ -30,14 +30,16 @@ get_chr=function(eqtl_fn){
 	as.integer(str_replace(unique(fread(eqtl_fn)$chr),'chr',''))
 }
 
-get_position=function(x){
+get_position=function(x,genome){
     stopifnot('rsid' %in% colnames(x))
     res = dbGetQuery(
-        conn = locuscompare_pool,
-        statement = sprintf(
-        "select rsid, chr, pos 
-		from tkg_p3v5a 
-		where rsid in ('%s')",paste0(x$rsid,collapse="','")
+		conn = locuscompare_pool,
+		statement = sprintf(
+			"select rsid, chr, pos 
+			from %s 
+			where rsid in ('%s')",
+			genome,
+			paste0(x$rsid,collapse="','")
         )
     )
     y=merge(x,res,by='rsid')
@@ -187,39 +189,44 @@ assign_size=function(merged,snp){
 }
 
 make_combined_plot=function(merged,title1,title2,ld,snp=NULL){
-	if (is.null(snp)){
-		snp=merged[which.min(pval1+pval2),rsid]
-	} else {
-		if(!snp%in%merged$rsid){
-			stop(sprintf('%s not found in %s',snp,in_fn1))
-		}
-	}
-	print(sprintf('INFO - %s',snp))
-
-	color=assign_color(merged$rsid,snp,ld)
-	shape=assign_shape(merged)
-	size=assign_size(merged)
-	merged[,label:=ifelse(rsid==snp,rsid,'')]
-
-	p1=make_locuscatter(merged,title1,title2,ld,color,shape,size)
-	p2=make_locuszoom(merged[,list(rsid,logp=logp1,label)],title1,ld,color,shape,size)
-	p2=p2+theme(axis.text.x=element_blank(),axis.title.x=element_blank())
-	p3=make_locuszoom(merged[,list(rsid,logp=logp2,label)],title2,ld,color,shape,size)
-	p4=plot_grid(p2,p3,align='v',nrow=2)
-	p5=plot_grid(p1,p4)
-	return(p5)
+  if (is.null(snp)){
+    snp=merged[which.min(pval1+pval2),rsid]
+  } else {
+    if(!snp%in%merged$rsid){
+      stop(sprintf('%s not found in %s',snp,in_fn1))
+    }
+  }
+  print(sprintf('INFO - %s',snp))
+
+  color=assign_color(merged$rsid,snp,ld)
+  shape=assign_shape(merged)
+  size=assign_size(merged)
+  merged[,label:=ifelse(rsid==snp,rsid,'')]
+
+  theme_set(theme_light(base_size=14))
+  p1=make_locuscatter(merged,title1,title2,ld,color,shape,size)
+  p2=make_locuszoom(merged[,list(rsid,logp=logp1,label)],title1,ld,color,shape,size)
+  p2=p2+theme(axis.text.x=element_blank(),axis.title.x=element_blank())
+  p3=make_locuszoom(merged[,list(rsid,logp=logp2,label)],title2,ld,color,shape,size)
+  p4=plot_grid(p2,p3,align='v',nrow=2)
+  p5=plot_grid(p1,p4)
+  return(p5)
 }
 
 
+
+
 make_locuscatter=function(merged,title1,title2,ld,color,shape,size,legend=TRUE){
 	p = ggplot(merged,aes(logp1,logp2))+
 		geom_point(aes(fill=rsid,size=rsid,shape=rsid),alpha=0.8)+
 		xlab(paste(title1,' -log10(P)'))+ylab(paste(title2,' -log10(P)'))+
 		scale_fill_manual(values=color,guide='none')+
 		scale_shape_manual(values=shape,guide='none')+
 		scale_size_manual(values=size,guide='none')+
-		geom_text(aes(label=label),hjust = 1.1)
-
+		geom_text(aes(label=label),hjust = 1.1)+
+	  theme(panel.background = element_rect(fill = "white"),axis.line = element_line(color = "black", size = 0.5), 
+	        axis.line.x = element_line(color = "black", size = 0.5),
+	        axis.line.y = element_line(color = "black", size = 0.5))
 	if (legend){
 		legend_box=data.frame(x=0.8,y=seq(0.4,0.2,-0.05))
 		p1=ggdraw(p)+geom_rect(data=legend_box,aes(xmin=x,xmax=x+0.05,ymin=y,ymax=y+0.05),color='black',fill=rev(c('blue4','skyblue','darkgreen','orange','red')))+
@@ -247,7 +254,8 @@ make_locuszoom=function(metal,title,ld,color,shape,size,y_string='logp'){
 		geom_text(aes(label=label),hjust = 1.1)+
 		xlab(paste0('chr',chr,' (Mb)'))+
 		ylab(paste(title,'\n-log10(P)'))+
-		theme(plot.margin=unit(c(0.5, 1, 0.5, 0.5), "lines"))
+		theme(panel.background = element_rect(fill = "white"),plot.margin=unit(c(0.5, 1, 0.5, 0.5), "lines"), axis.line = element_line(color = "black", size = 0.5),
+		      axis.line.x = element_line(color = "black", size = 0.5), axis.line.y = element_line(color = "black", size = 0.5))
 	return(p)
 }