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Last updated: 2022-11-18

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Knit directory: SingleCellMR/

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libraries

library(ggplot2)
library(viridis)
library(ggsci)
library(dplyr)
library(cowplot)
library(grid)
library(tidyr)
suppressMessages(library(reshape))
color_pal=ggsci::pal_nejm("default")(8)
colorvec<-c(Astrocytes=color_pal[1],
           Endothelial=color_pal[2],
           Excitatory=color_pal[3],
           Inhibitory=color_pal[4],Microglia=color_pal[5],
           ODC=color_pal[6],OPC=color_pal[7],Pericytes=color_pal[8])

FIGURE 1

coming soon

FIGURE 2

Figure 2a

coloc<-read.table("data/COLOC_MR_RESULTS/2022-10-25_FULL_COLOC_RES.txt")
x<-coloc[coloc$GWAS %in% "AD",]
x<-coloc[coloc$GWAS %in% "AD",]


genes<-x[x$PP.H4.abf>0.5,]$gene
x<-x[x$gene %in% genes,]
x$gene<-factor(x$gene,levels=unique(x$gene))

g<-ggplot(x,aes(x=celltype,y=gene,fill=PP.H4.abf))
g<-g+geom_tile(aes(fill=round(PP.H4.abf,2)),colour="black")+
geom_text(aes(label = round(PP.H4.abf, 2)),size=5*0.36,family="Helvetica")+
scale_fill_viridis()+
theme_classic()+
scale_y_discrete(limits=rev,expand = c(0, 0))+
scale_x_discrete(expand = c(0, 0),position="top")+
xlab("Alzheimer's Disease")
g

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Version	Author	Date
8f071f3	Alexander Haglund	2022-11-18

Figure 2b

Figure 2c

Figure 2e

Figure 2d

FIGURE 3

The code presented here is in step 5 (Epigenetic Intersection) of the downstream results section. The basic syntax is a geom_tile() function in ggplot with colours matching cell-types. More in data/MARKDOWN/helper_funcs.r

This is only for Fig 3.a - Fig 3.c and Fig 3.d were made using the UCSC track browser.

indir<-"data/EXT_DATASETS//RESULTS/"
fig_dir<-"FIGURES/Figure_3/"

g1<-readRDS(paste0(indir,"oligo_intersect_ggobject.rds"))
g2<-readRDS(paste0(indir,"Excneuron_intersect_ggobject.rds"))
g3<-readRDS(paste0(indir,"Inneuron_intersect_ggobject.rds"))
g4<-readRDS(paste0(indir,"microglia_intersect_ggobject.rds"))

g1<-g1+theme(legend.position = "none")
g2<-g2+theme(legend.position = "none")
g3<-g3+theme(legend.position = "none")
g4<-g4+theme(legend.position = "none")

Oligo

g1

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Version	Author	Date
8f071f3	Alexander Haglund	2022-11-18

ExcNeur

g2

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Version	Author	Date
8f071f3	Alexander Haglund	2022-11-18

InNeur

g3

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Version	Author	Date
8f071f3	Alexander Haglund	2022-11-18

Microglia

g4

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Version	Author	Date
8f071f3	Alexander Haglund	2022-11-18

FIGURE 4

Figure 4a

bind data together

#bind data together

pqtl<-read.table("data/TABLES/pQTL_table.txt")
stitch<-read.table("data/TABLES//stitch_table.txt")
dgidb<-read.table("data/TABLES/dgidb_table.txt")
opentargets<-read.table("data/TABLES/OpenTargets_table.txt")
coloc<-read.table("data/COLOC_MR_RESULTS//2022-10-25_FULL_COLOC_RES.txt")
full<-read.table("data/COLOC_MR_RESULTS//2022-10-25_FULL_MR_RES.txt")
full<-full[full$IVW<0.05,]
full$trait_gene<-paste0(full$GWAS,"_",full$gene)
full$IVW_dir<-sapply(full$IVW_beta,function(x){
    if(x>0){
        return("positive")
        }else{
        return("negative")
        }
    })
direction_vector<-vector()
for(i in 1:nrow(full)){
    tmp<-full[full$trait_gene %in% full$trait_gene[i],]
    betas<-tmp$IVW_beta
    
    if(all(betas>0)==TRUE){
    dir<-"positive"
    } else if(all(betas<0)==TRUE){
    dir<-"negative"
    }else{
        dir<-"N/A"
        }
    direction_vector<-c(direction_vector,dir)    
        }
full$IVW_dir<-direction_vector    


coloc$trait_gene_ct<-paste0(coloc$GWAS,"_",coloc$gene,"_",coloc$celltype)
trait_gene_ct<-paste0(pqtl$GWAS,"_",pqtl$gene,"_",pqtl$celltype)
coloc<-coloc[match(trait_gene_ct,coloc$trait_gene_ct),]

plot_df<-data.frame(gene_trait=paste0(pqtl$GWAS,".",pqtl$gene),
                    pQTL=pqtl$pQTL_hit,
                    STITCH=stitch$STITCH_intersect,
                    DGidb=dgidb$DGIDB_intersect,
                    OpenTargets=opentargets$OpenTargets_disease_hit,
                   coloc=coloc$PP.H4.abf,
                   celltype=pqtl$celltype,
                   IVW_dir=full$IVW_dir)

prep plots

n_rows<-nrow(plot_df)
half<-round(n_rows/2)

#split in two (plot is too big otherwise)
plot_df1<-plot_df[1:half,c("gene_trait","pQTL","STITCH","DGidb","OpenTargets")]
melt_df<-melt(plot_df1,id=c("gene_trait"))
ggplot_mainplot1<-ggplot(melt_df,aes(x=variable,y=gene_trait,fill=value))+geom_tile(color="black")+
scale_fill_manual(values=c("#c8c8c8","#A6CEE3","#1F78B4"))+scale_x_discrete(expand=c(0,0))


plot_df2<-plot_df[half:n_rows,c("gene_trait","pQTL","STITCH","DGidb","OpenTargets")]
melt_df<-melt(plot_df2,id=c("gene_trait"))
ggplot_mainplot2<-ggplot(melt_df,aes(x=variable,y=gene_trait,fill=value))+geom_tile(color="black")+
scale_fill_manual(values=c("#c8c8c8","#A6CEE3","#1F78B4"))+scale_x_discrete(expand=c(0,0))



##coloc PPH4 bar
coloc_bar<-plot_df[,c("gene_trait","coloc")]

coloc_bar1<-coloc_bar[1:half,]
melt_df<-melt(coloc_bar1,id=c("gene_trait"))
ggplot_coloc1<-ggplot(melt_df,aes(x=variable,y=gene_trait,fill=value))+geom_tile(color="black")+
scale_fill_viridis(limits=c(0.5,1))

coloc_bar2<-coloc_bar[half:n_rows,]
melt_df<-melt(coloc_bar2,id=c("gene_trait"))
ggplot_coloc2<-ggplot(melt_df,aes(x=variable,y=gene_trait,fill=value))+geom_tile(color="black")+
scale_fill_viridis(limits=c(0.5,1))

##celltype MR direction

celltype_dir<-plot_df[,c("gene_trait","celltype","IVW_dir")]
celltype_dir1<-celltype_dir[1:half,]

ggplot_celltype_dir1<-ggplot(celltype_dir1,aes(x=IVW_dir,y=gene_trait,fill=celltype,group=celltype))+
geom_point(shape=22,size=2,stroke=0.1,position=position_dodge(w=0.7))+
scale_fill_manual(values = colorvec)+
theme_classic()+
geom_vline(xintercept=0,linetype="dotted")

celltype_dir2<-celltype_dir[half:n_rows,]

ggplot_celltype_dir2<-ggplot(celltype_dir2,aes(x=IVW_dir,y=gene_trait,fill=celltype,group=celltype))+
geom_point(shape=22,size=2,stroke=0.1,position=position_dodge(w=0.7))+
scale_fill_manual(values = colorvec)+
theme_classic()+
geom_vline(xintercept=0,linetype="dotted")

##direction only
ivw_dir<-plot_df[,c("gene_trait","IVW_dir")]
ivw_dir$trait<-"gwas"
ivw_dir1<-ivw_dir[1:half,]

ggplot_ivwdir1<-ggplot(ivw_dir1,aes(y=gene_trait,x=trait,fill=IVW_dir,group=IVW_dir))+geom_tile(colour="black")+
scale_fill_manual(values = c("#c8c8c8","#F8766D","#00BFC4"),guide = guide_legend(reverse = TRUE))+
theme_classic()


ivw_dir<-plot_df[,c("gene_trait","IVW_dir")]
ivw_dir$trait<-"gwas"
ivw_dir2<-ivw_dir[half:n_rows,]

ggplot_ivwdir2<-ggplot(ivw_dir2,aes(y=gene_trait,x=trait,fill=IVW_dir,group=IVW_dir))+geom_tile(colour="black")+
scale_fill_manual(values = c("#F8766D","#00BFC4"),guide = guide_legend(reverse = TRUE))+
theme_classic()



##celltype bar
celltype_bar<-plot_df[,c("gene_trait","celltype")]

celltype_bar1<-celltype_bar[1:half,]
test<-celltype_bar1 %>% 
count(gene_trait,celltype,name="count") %>% 
complete(gene_trait,celltype)
newvec<-vector()
for(i in 1:nrow(test)){
    if(is.na(test$count[i])){
        newvec<-c(newvec,NA)
        }else{
        newvec<-c(newvec,test$celltype[i])
        }
    }
test$new<-newvec
# melt_df<-melt(celltype_bar1,id=c("gene_trait"))
# df2 = celltype_bar1 %>% complete(gene_trait,celltype)
ggplot_celltype1<-ggplot(test,aes(x=celltype,y=gene_trait,fill=new))+geom_tile(color="black")+
scale_fill_manual(values=colorvec,na.value="white")

celltype_bar2<-celltype_bar[half:n_rows,]
test<-celltype_bar2 %>% 
count(gene_trait,celltype,name="count") %>% 
complete(gene_trait,celltype)
newvec<-vector()
for(i in 1:nrow(test)){
    if(is.na(test$count[i])){
        newvec<-c(newvec,NA)
        }else{
        newvec<-c(newvec,test$celltype[i])
        }
    }
test$new<-newvec
# melt_df<-melt(celltype_bar2,id=c("gene_trait"))
ggplot_celltype2<-ggplot(test,aes(x=celltype,y=gene_trait,fill=new))+geom_tile(color="black")+
scale_fill_manual(values=colorvec,na.value="white")

plot1

ggplot_mainplot1<-ggplot_mainplot1+theme_classic()+
theme(axis.text.x=element_text(size=5,face="bold",angle=45,vjust=0.8,hjust=0.8,family="Helvetica"),
      axis.text.y=element_text(size=5,face="bold",vjust=0.8,family="Helvetica"),axis.title.y=element_blank(),
      axis.line.y=element_blank(),axis.line.x=element_blank(),
      axis.title.x=element_blank(),legend.key.size=unit(0.7,"cm"),
      legend.title=element_blank(),
      legend.text=element_text(size=5),
      panel.background = element_rect(fill='transparent'),
      plot.background = element_rect(fill='transparent', color=NA),
      panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
      legend.background = element_rect(fill='transparent'),
      legend.key.height= unit(0.3, 'cm'),
      legend.key.width= unit(0.2, 'cm'))#

ggplot_celltype_dir1<-ggplot_celltype_dir1+theme_classic()+
theme(axis.text.x=element_text(size=5,face="bold",angle=45,vjust=0.8,hjust=0.8,family="Helvetica"),
      axis.text.y=element_blank(),axis.title.y=element_blank(),axis.ticks.y=element_blank(),
      axis.line.y=element_blank(),axis.line.x=element_blank(),
      axis.title.x=element_blank(),legend.key.size=unit(0.7,"cm"),
      legend.position="none",panel.grid.major.y=element_line(size=0.3,colour="grey"),
      legend.text=element_text(size=5),
      panel.background = element_rect(fill='transparent'),
      plot.background = element_rect(fill='transparent', color=NA),
      legend.background = element_rect(fill='transparent'),
      legend.key.height= unit(0.3, 'cm'),
      legend.key.width= unit(0.2, 'cm'))#

ggplot_ivwdir1<-ggplot_ivwdir1+theme_classic()+
theme(axis.text.x=element_blank(),
      axis.text.y=element_blank(),axis.title.y=element_blank(),axis.ticks.y=element_blank(),
      axis.ticks.x=element_blank(),
      axis.line.y=element_blank(),axis.line.x=element_blank(),
      axis.title.x=element_blank(),legend.key.size=unit(0.7,"cm"),
      legend.text=element_text(size=5), legend.title=element_text(size=5),
      panel.background = element_rect(fill='transparent'),
      plot.background = element_rect(fill='transparent', color=NA),
      legend.background = element_rect(fill='transparent'),
      legend.key.height= unit(0.3, 'cm'),
      legend.key.width= unit(0.2, 'cm'))#

ggplot_coloc1<-ggplot_coloc1+theme_classic()+
theme(axis.text.x=element_blank(),axis.ticks.x=element_blank(),
      axis.text.y=element_blank(),axis.title.y=element_blank(),axis.ticks.y=element_blank(),
      axis.line.y=element_blank(),axis.line.x=element_blank(),
      axis.title.x=element_blank(),legend.key.size=unit(0.7,"cm"),
      legend.title=element_blank(),
      legend.text=element_text(size=5),
      panel.background = element_rect(fill='transparent'),
      plot.background = element_rect(fill='transparent', color=NA),
      panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
      legend.background = element_rect(fill='transparent'),
      legend.key.height= unit(0.3, 'cm'),
      legend.key.width= unit(0.2, 'cm'))#

ggplot_celltype1<-ggplot_celltype1+theme_classic()+
theme(axis.text.x=element_text(size=5,face="bold",angle=45,vjust=0.8,hjust=0.8,family="Helvetica"),
      axis.text.y=element_blank(),axis.title.y=element_blank(),axis.ticks.y=element_blank(),
      axis.line.y=element_blank(),axis.line.x=element_blank(),
      axis.title.x=element_blank(),legend.key.size=unit(0.7,"cm"),
      legend.title=element_blank(),
      legend.text=element_text(size=5),
      panel.background = element_rect(fill='transparent'),
      plot.background = element_rect(fill='transparent', color=NA),
      legend.background = element_rect(fill='transparent'),
      legend.key.height= unit(0.3, 'cm'),
      legend.key.width= unit(0.2, 'cm'))#

coloc_legend<-get_legend(ggplot_coloc1)
ggplot_mainplot1_legend<-get_legend(ggplot_mainplot1)
celltype_legend<-get_legend(ggplot_celltype1)
ivw_dir<-get_legend(ggplot_ivwdir1)


ggplot_coloc1<-ggplot_coloc1+theme(plot.margin = unit(c(0,0,0,0), "cm"),legend.position = "none")
ggplot_ivwdir1<-ggplot_ivwdir1+theme(plot.margin = unit(c(0,0,0,0), "cm"),legend.position = "none")
ggplot_mainplot1<-ggplot_mainplot1+theme(plot.margin = unit(c(0,0,0,0), "cm"),legend.position = "none")
ggplot_celltype1<-ggplot_celltype1+theme(plot.margin = unit(c(0,0,0,0), "cm"),legend.position="none")

g<-plot_grid(ggplot_mainplot1,ggplot_celltype1,ggplot_ivwdir1, align = "h", ncol =3, rel_widths = c(0.008,0.005,0.001))
g

Past versions of unnamed-chunk-10-1.png

Version	Author	Date
8f071f3	Alexander Haglund	2022-11-18

plot2

ggplot_mainplot2<-ggplot_mainplot2+theme_classic()+
theme(axis.text.x=element_text(size=5,face="bold",angle=45,vjust=0.8,hjust=0.8,family="Helvetica"),
      axis.text.y=element_text(size=5,face="bold",vjust=0.8,family="Helvetica"),axis.title.y=element_blank(),
      axis.line.y=element_blank(),axis.line.x=element_blank(),
      axis.title.x=element_blank(),legend.key.size=unit(0.7,"cm"),
      legend.title=element_blank(),
      legend.text=element_text(size=5),
      panel.background = element_rect(fill='transparent'),
      plot.background = element_rect(fill='transparent', color=NA),
      panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
      legend.background = element_rect(fill='transparent'),legend.box.background = element_rect(fill='transparent'))#

ggplot_coloc2<-ggplot_coloc2+theme_classic()+
theme(axis.text.x=element_blank(),axis.ticks.x=element_blank(),
      axis.text.y=element_blank(),axis.title.y=element_blank(),axis.ticks.y=element_blank(),
      axis.line.y=element_blank(),axis.line.x=element_blank(),
      axis.title.x=element_blank(),legend.key.size=unit(0.7,"cm"),
      legend.title=element_blank(),
      legend.text=element_text(size=5),
      panel.background = element_rect(fill='transparent'),
      plot.background = element_rect(fill='transparent', color=NA),
      legend.background = element_rect(fill='transparent'),legend.box.background = element_rect(fill='transparent'))#

ggplot_celltype_dir2<-ggplot_celltype_dir2+theme_classic()+
theme(axis.text.x=element_text(size=5,face="bold",angle=45,vjust=0.8,hjust=0.8,family="Helvetica"),
      axis.text.y=element_blank(),axis.title.y=element_blank(),axis.ticks.y=element_blank(),
      axis.line.y=element_blank(),axis.line.x=element_blank(),
      axis.title.x=element_blank(),legend.key.size=unit(0.7,"cm"),
      legend.position="none",panel.grid.major.y=element_line(size=0.3,colour="grey"),
      legend.text=element_text(size=5),
      panel.background = element_rect(fill='transparent'),
      plot.background = element_rect(fill='transparent', color=NA),
      legend.background = element_rect(fill='transparent'),
      legend.key.height= unit(0.3, 'cm'),
      legend.key.width= unit(0.2, 'cm'))#

ggplot_ivwdir2<-ggplot_ivwdir2+theme_classic()+
theme(axis.text.x=element_blank(),
      axis.text.y=element_blank(),axis.title.y=element_blank(),axis.ticks.y=element_blank(),
      axis.ticks.x=element_blank(),
      axis.line.y=element_blank(),axis.line.x=element_blank(),
      axis.title.x=element_blank(),legend.key.size=unit(0.7,"cm"),
      legend.text=element_text(size=5), legend.title=element_text(size=5),
      panel.background = element_rect(fill='transparent'),
      plot.background = element_rect(fill='transparent', color=NA),
      legend.background = element_rect(fill='transparent'),
      legend.key.height= unit(0.3, 'cm'),
      legend.key.width= unit(0.2, 'cm'))#

ggplot_celltype2<-ggplot_celltype2+theme_classic()+
theme(axis.text.x=element_text(size=5,face="bold",angle=45,vjust=0.8,hjust=0.8,family="Helvetica"),
      axis.text.y=element_blank(),axis.title.y=element_blank(),axis.ticks.y=element_blank(),
      axis.line.y=element_blank(),axis.line.x=element_blank(),
      axis.title.x=element_blank(),legend.key.size=unit(0.7,"cm"),
      legend.title=element_blank(),
      legend.text=element_text(size=5),
      panel.background = element_rect(fill='transparent'),
      plot.background = element_rect(fill='transparent', color=NA),
      panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
      legend.background = element_rect(fill='transparent'),legend.box.background = element_rect(fill='transparent'))#

ggplot_coloc2<-ggplot_coloc2+theme(plot.margin = unit(c(0,0,0,0), "cm"),legend.position = "none")
ggplot_ivwdir2<-ggplot_ivwdir2+theme(plot.margin = unit(c(0,0,0,0), "cm"),legend.position = "none")
ggplot_mainplot2<-ggplot_mainplot2+theme(plot.margin = unit(c(0,0,0,0), "cm"),legend.position = "none")
ggplot_celltype2<-ggplot_celltype2+theme(plot.margin = unit(c(0,0,0,0), "cm"),legend.position="none")


g<-plot_grid(ggplot_mainplot2,ggplot_celltype2,ggplot_ivwdir2, align = "h", ncol =3, rel_widths = c(0.008,0.005,0.001))
g

Past versions of unnamed-chunk-11-1.png

Version	Author	Date
8f071f3	Alexander Haglund	2022-11-18

FIGURE 5

Figure 5a

full<-read.table("data/COLOC_MR_RESULTS//2022-10-25_FULL_MR_RES.txt")
full<-full[full$IVW<0.05,]
full$trait_gene<-paste0(full$GWAS,"_",full$gene)
full$IVW_dir<-sapply(full$IVW_beta,function(x){
    if(x>0){
        return("CAUSAL")
        }else{
        return("PROTECTIVE")
        }
    })

tmp<-full[full$GWAS=="AD",]
tmp<-tmp[order(tmp$celltype),]
tmp$gene<-factor(tmp$gene,levels=unique(tmp$gene))
color_pal=ggsci::pal_nejm("default")(8)
colorvec<-c(Astrocytes=color_pal[1],
           Endothelial=color_pal[2],
           Excitatory=color_pal[3],
           Inhibitory=color_pal[4],Microglia=color_pal[5],
           ODC=color_pal[6],OPC=color_pal[7],Pericytes=color_pal[8])

g<-ggplot(tmp,aes(y=gene,x=IVW_beta,fill=celltype))+
geom_point(colour="black",shape=21,stroke=0.3,size=2)+
scale_fill_manual(values = colorvec)+
theme_classic()+
geom_vline(xintercept=0,linetype="dotted")+scale_x_continuous(limits=c(-0.6,0.6))
g2<-g+
theme(text=element_text(family="Helvetica",size=5),legend.text = element_text(family="Helvetica",size=5,face="bold"),
      legend.title=element_blank(),
      legend.spacing.y = unit(-1, 'cm'),axis.text.y=element_text(family="Helvetica",size=5,face="bold"))+guides(fill = guide_legend(byrow = TRUE))
g2

Past versions of unnamed-chunk-12-1.png

Version	Author	Date
8f071f3	Alexander Haglund	2022-11-18

Figure 5b

full<-read.table("data/COLOC_MR_RESULTS//2022-10-25_FULL_MR_RES.txt")
plot_df<-data.frame()
for(i in 1:length(unique(full$GWAS))){
    gwas<-unique(full$GWAS)[i]
    tmp_full<-full[full$GWAS==gwas,]
    cellvec<-as.vector(table(tmp_full$celltype))
    plot_df<-rbind(plot_df,data.frame(gwas=gwas,
                                      celltype=names(table(tmp_full$celltype)),
                                      occurrence=cellvec))
    }
g<-ggplot(data=plot_df,aes(y=occurrence,x=gwas,fill=celltype))+
geom_bar(stat="identity",colour="black",size=0.25)+
scale_fill_manual(values=color_pal)+theme_classic()+
geom_text(aes(label=occurrence),family="Helvetica",size=5*0.36, position = position_stack(vjust = 0.5))+
theme_classic()+scale_y_continuous(expand=c(0,0))+
labs(title="Cell-type proportions in MR results",size=7,family="Helvetica")+
theme(text=element_text(size=7,family="Helvetica"),axis.text.x=element_text(size=5,face="bold",angle=90),
                                  axis.text.y=element_text(size=5),
                                  axis.title.y=element_blank(),
                                 axis.title.x=element_blank(),legend.position="none",
     title=element_text(size=7,face="bold"))
g

Past versions of unnamed-chunk-13-1.png

Version	Author	Date
8f071f3	Alexander Haglund	2022-11-18

Figure 5c

full<-read.table("data/COLOC_MR_RESULTS//2022-10-25_FULL_MR_RES.txt")
full$celltype_gene<-paste0(full$celltype,".",full$gene)
scz<-full[full$GWAS=="SCZ",]
iq<-full[full$GWAS=="IQ",]
common<-intersect(iq$celltype_gene,scz$celltype_gene)

##remove ct/gene combinations in other traits - we are only interested in the SCZ/IQ overlap
# filtered<-full[full$celltype_gene %in% common,]
# filtered<-filtered[!filtered$GWAS %in% c("SCZ","IQ"),]
# to_exclude<-unique(filtered$celltype_gene)
# common<-common[!common %in% to_exclude]



#filter both
scz<-scz[match(common,scz$celltype_gene),]
iq<-iq[match(common,iq$celltype_gene),]
df<-data.frame(celltype_gene=common,IQ=iq$IVW_beta,SCZ=scz$IVW_beta)


##now plot
ylims=c(-0.2,0.2)
xlims=c(-0.7,0.7)

g<-ggplot(df,aes(x=SCZ,y=IQ,fill=celltype_gene))+
geom_point(shape=21,size=2)+
scale_y_continuous(limits=ylims)+
scale_x_continuous(limits=xlims)+
geom_vline(xintercept =0,linetype="dotted")+
geom_hline(yintercept =0,linetype="dotted")+theme_classic()+
theme(text=element_text(size=5,family="Helvetica"),legend.title=element_blank(),legend.text = element_text(family="Helvetica",size=5,face="bold"),legend.spacing.y = unit(-1, 'cm'))+
xlab("SCZ - MR beta")+ylab("IQ - MR beta")+
guides(fill = guide_legend(byrow = TRUE))
g

Past versions of unnamed-chunk-14-1.png

Version	Author	Date
8f071f3	Alexander Haglund	2022-11-18

Figure 5d

full<-read.table("data/COLOC_MR_RESULTS//2022-10-25_FULL_MR_RES.txt")
full$celltype_gene<-paste0(full$celltype,".",full$gene)
scz<-full[full$GWAS=="SCZ",]
neur<-full[full$GWAS=="NEUR",]
common<-intersect(neur$celltype_gene,scz$celltype_gene)

# filtered<-full[full$celltype_gene %in% common,]
# filtered<-filtered[!filtered$GWAS %in% c("SCZ","NEUR"),]
# to_exclude<-unique(filtered$celltype_gene)
# common<-common[!common %in% to_exclude]


#filter both
scz<-scz[match(common,scz$celltype_gene),]
neur<-neur[match(common,neur$celltype_gene),]
df<-data.frame(celltype_gene=common,NEUR=neur$IVW_beta,SCZ=scz$IVW_beta)


##now plot
ylims=c(-0.2,0.2)
xlims=c(-0.8,0.8)

g<-ggplot(df,aes(x=SCZ,y=NEUR,fill=celltype_gene))+
geom_point(shape=21,size=2)+
scale_y_continuous(limits=ylims)+
scale_x_continuous(limits=xlims)+
geom_vline(xintercept =0,linetype="dotted")+
geom_hline(yintercept =0,linetype="dotted")+theme_classic()+
theme(text=element_text(size=5,family="Helvetica"),legend.text = element_text(family="Helvetica",size=5,face="bold"),legend.title=element_blank(),legend.spacing.y = unit(-1, 'cm'))+
xlab("SCZ - MR beta")+ylab("NEUR - MR beta")+guides(fill = guide_legend(byrow = TRUE))
g

Past versions of unnamed-chunk-15-1.png

Version	Author	Date
8f071f3	Alexander Haglund	2022-11-18

Session information

sessionInfo()

R version 4.0.5 (2021-03-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS/LAPACK: /home/ah3918/anaconda3/envs/ODIN3/lib/libopenblasp-r0.3.12.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] reshape_0.8.9     tidyr_1.2.1       cowplot_1.1.1     dplyr_1.0.9      
[5] ggsci_2.9         viridis_0.6.2     viridisLite_0.4.1 ggplot2_3.3.6    
[9] workflowr_1.7.0  

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.2 xfun_0.32        bslib_0.4.0      purrr_0.3.4     
 [5] colorspace_2.0-3 vctrs_0.5.0      generics_0.1.3   htmltools_0.5.3 
 [9] yaml_2.3.5       utf8_1.2.2       rlang_1.0.6      jquerylib_0.1.4 
[13] later_1.2.0      pillar_1.8.1     glue_1.6.2       withr_2.5.0     
[17] DBI_1.1.3        plyr_1.8.7       lifecycle_1.0.3  stringr_1.4.0   
[21] munsell_0.5.0    gtable_0.3.1     evaluate_0.16    labeling_0.4.2  
[25] knitr_1.39       callr_3.7.1      fastmap_1.1.0    httpuv_1.6.5    
[29] ps_1.7.1         fansi_1.0.3      highr_0.9        Rcpp_1.0.9      
[33] promises_1.2.0.1 scales_1.2.1     cachem_1.0.6     jsonlite_1.8.0  
[37] farver_2.1.1     fs_1.5.2         gridExtra_2.3    digest_0.6.30   
[41] stringi_1.7.8    processx_3.7.0   getPass_0.2-2    rprojroot_2.0.3 
[45] cli_3.4.1        tools_4.0.5      magrittr_2.0.3   sass_0.4.2      
[49] tibble_3.1.8     whisker_0.4      pkgconfig_2.0.3  ellipsis_0.3.2  
[53] assertthat_0.2.1 rmarkdown_2.15   httr_1.4.3       rstudioapi_0.13 
[57] R6_2.5.1         git2r_0.30.1     compiler_4.0.5