library(data.table)
library(ggplot2)
library(readxl)
library(cowplot)
library(ggrepel)
library(grid)
options(ggrepel.max.overlaps=Inf)


#Figure 1
data1 <- read.csv("INPUT_PATH/TRAITS_VS_GWAS2_SN_PPV.csv", head=T, stringsAsFactors=F) 
#looks okay 

ppi <- 300
png(filename="OUTPUT_PATH/Figure1.png", width=8, height=8, unit="in", res=ppi)
.labs <- data1$Method2
grob1 <- grobTree(textGrob("I", x=0.55, y=0.55, hjust=0, gp=gpar(col="red", fontsize=13, fontface="bold")))
grob2 <- grobTree(textGrob("II", x=0.44, y=0.55, hjust=0, gp=gpar(col="red", fontsize=13, fontface="bold")))
grob3 <- grobTree(textGrob("III", x=0.43, y=0.45, hjust=0, gp=gpar(col="red", fontsize=13, fontface="bold")))
grob4 <- grobTree(textGrob("IV", x=0.55, y=0.45, hjust=0, gp=gpar(col="red", fontsize=13, fontface="bold")))
b <- ggplot(data1, aes(x = SN, y = PPV)) 
b + geom_point(aes(color = Trait)) + geom_hline(yintercept=0.50) + geom_vline(xintercept=0.50) + theme_bw() + theme(panel.grid.major=element_blank(), panel.grid.minor=element_blank()) +
  geom_text_repel(aes(label = .labs,  color = Trait), size = 3, max.overlaps=Inf)+ scale_x_continuous(limits=c(0,1)) + scale_y_continuous(limits=c(0,1)) + 
  scale_color_manual(values = c("#CC79A7", "#009E73", "#E69F00", "#0072B2", "#000000")) + ggtitle("SN vs PPV for Nominated Loci (+/-500kb)") + theme(plot.title=element_text(hjust=0.5)) + annotation_custom(grob1) + annotation_custom(grob2) + annotation_custom(grob3) + annotation_custom(grob4)

dev.off()





#Figure 4
grob1 <- grobTree(textGrob("I", x=0.55, y=0.55, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob2 <- grobTree(textGrob("II", x=0.44, y=0.55, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob3 <- grobTree(textGrob("III", x=0.43, y=0.45, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob4 <- grobTree(textGrob("IV", x=0.55, y=0.45, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))

data3 <- read.csv("INPUT_PATH/PGC_VS_GWAS3.csv", head=T, stringsAsFactors=F) 
ppi <- 300
png(filename="OUTPUT_PATH/Figure4.png", width=8, height=8, unit="in", res=ppi)
.labs <- data3$Method2
b <- ggplot(data3, aes(x = SN, y = PPV)) 
b + geom_point(aes(color = Trait)) + geom_hline(yintercept=0.50) + geom_vline(xintercept=0.50) + theme_bw() + theme(panel.grid.major=element_blank(), panel.grid.minor=element_blank()) +
  geom_text_repel(aes(label = .labs,  color = Trait), size = 3, max.overlaps=Inf)+ scale_x_continuous(limits=c(0,1)) + scale_y_continuous(limits=c(0,1)) + 
  scale_color_manual(values = c("#CC79A7", "#009E73", "#0072B2" )) + ggtitle("SN vs PPV for PGC Nominated Loci (+/-500kb)") + theme(plot.title=element_text(hjust=0.5)) + annotation_custom(grob1) + annotation_custom(grob2) + annotation_custom(grob3) + annotation_custom(grob4)


dev.off()

###############################################
# Figure SF1 



data2 <- subset(data1, Trait %in% c("BPD", "SCZ", "MDD"))
ppi <- 300
png(filename="OUTPUT_PATH/FigureSF1.png", width=8, height=8, unit="in", res=ppi)
.labs <- data2$Method2
b <- ggplot(data2, aes(x = SN, y = PPV)) 
b + geom_point(aes(color = Trait)) + geom_hline(yintercept=0.50) + geom_vline(xintercept=0.50) + theme_bw() + theme(panel.grid.major=element_blank(), panel.grid.minor=element_blank()) +
  geom_text_repel(aes(label = .labs,  color = Trait), size = 3, max.overlaps=Inf)+ scale_x_continuous(limits=c(0,1)) + scale_y_continuous(limits=c(0,1)) + 
  scale_color_manual(values = c("#CC79A7", "#009E73", "#0072B2" )) + ggtitle("SN vs PPV for PGC Nominated Loci (+/-500kb)") + theme(plot.title=element_text(hjust=0.5)) + annotation_custom(grob1) + annotation_custom(grob2) + annotation_custom(grob3) + annotation_custom(grob4)


dev.off()


##############################################

#Figure SF2  
#plot of FDR sensitivity analysis 
grob1 <- grobTree(textGrob("I", x=0.55, y=0.55, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob2 <- grobTree(textGrob("II", x=0.44, y=0.55, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob3 <- grobTree(textGrob("III", x=0.43, y=0.45, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob4 <- grobTree(textGrob("IV", x=0.55, y=0.45, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))

data4 <- read.csv("INPUT_PATH/PGCONLY_FDR.csv", head=T, stringsAsFactors=F) 
ppi <- 300
png(filename="OUTPUT_PATH/FigureSF2.png", width=8, height=8, unit="in", res=ppi)
.labs <- data4$Method
b <- ggplot(data4, aes(x = SN, y = PPV)) 
b + geom_point(aes(color = Trait)) + geom_hline(yintercept=0.50) + geom_vline(xintercept=0.50) + theme_bw() + theme(panel.grid.major=element_blank(), panel.grid.minor=element_blank()) +
  geom_text_repel(aes(label = .labs,  color = Trait), size = 3, max.overlaps=Inf)+ scale_x_continuous(limits=c(0,1)) + scale_y_continuous(limits=c(0,1)) + 
  scale_color_manual(values = c("#CC79A7", "#009E73", "#0072B2" )) + ggtitle("SN vs PPV for PGC Nominated Loci (+/-500kb)") + theme(plot.title=element_text(hjust=0.5)) + annotation_custom(grob1) + annotation_custom(grob2) + annotation_custom(grob3) + annotation_custom(grob4)
dev.off()



###########################################
#PGC overlap sensitivities 
scz <- read.csv("INPUT_PATH/SCZ_OVERLAP_FILE.csv", head=T, stringsAsFactors=F)
mdd <- read.csv("INPUT_PATH/MDD_OVERLAP_FILE.csv", head=T, stringsAsFactors=F)
bpd <- read.csv("INPUT_PATH/BPD_OVERLAP_FILE.csv", head=T, stringsAsFactors=F)
mpv <- read.csv("INPUT_PATH/MPV_OVERLAP_FILE.csv", head=T, stringsAsFactors=F)
wbc <- read.csv("INPUT_PATH/WBC_OVERLAP_FILE.csv", head=T, stringsAsFactors=F)


grob1 <- grobTree(textGrob("I", x=0.55, y=0.55, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob2 <- grobTree(textGrob("II", x=0.44, y=0.55, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob3 <- grobTree(textGrob("III", x=0.43, y=0.45, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob4 <- grobTree(textGrob("IV", x=0.55, y=0.45, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))

#Figure S3a 
ppi <- 300
png(filename="OUTPUT_PATH/FigureS3a.png", width=8, height=8, unit="in", res=ppi)
.labs <- bpd$Method4
b <- ggplot(bpd, aes(x = SN, y = PPV)) 
b + geom_point(aes(color = Overlap)) + geom_hline(yintercept=0.50) + geom_vline(xintercept=0.50) + theme_bw() + theme(panel.grid.major=element_blank(), panel.grid.minor=element_blank()) +
  geom_text_repel(aes(label = .labs,  color = Overlap), size = 3, max.overlaps=Inf)+ scale_x_continuous(limits=c(0,1)) + scale_y_continuous(limits=c(0,1)) + 
  scale_color_manual(labels=c("1 base pair", "250kb", "500kb", "750kb"), values = c("red", "blue", "green", "purple", "black")) + ggtitle("SN vs PPV for Nominated Loci (+/-500kb), BPD") + theme(plot.title=element_text(hjust=0.5)) + annotation_custom(grob1) + annotation_custom(grob2) + annotation_custom(grob3) + annotation_custom(grob4)


dev.off()

#Figure S3b 
ppi <- 300
png(filename="OUTPUT_PATH/FigureS3b.png", width=8, height=8, unit="in", res=ppi)
.labs <- mdd$Method4
b <- ggplot(mdd, aes(x = SN, y = PPV)) 
b + geom_point(aes(color = Overlap)) + geom_hline(yintercept=0.50) + geom_vline(xintercept=0.50) + theme_bw() + theme(panel.grid.major=element_blank(), panel.grid.minor=element_blank()) +
  geom_text_repel(aes(label = .labs,  color = Overlap), size = 3, max.overlaps=Inf)+ scale_x_continuous(limits=c(0,1)) + scale_y_continuous(limits=c(0,1)) + 
  scale_color_manual(labels=c("1 base pair", "250kb", "500kb", "750kb"), values = c("red", "blue", "green", "purple", "black")) + ggtitle("SN vs PPV for Nominated Loci (+/-500kb), MDD") + theme(plot.title=element_text(hjust=0.5)) + annotation_custom(grob1) + annotation_custom(grob2) + annotation_custom(grob3) + annotation_custom(grob4)

dev.off()

#Figure S3c 
ppi <- 300
png(filename="OUTPUT_PATH/FigureS3c.png", width=8, height=8, unit="in", res=ppi)
.labs <- scz$Method4
b <- ggplot(scz, aes(x = SN, y = PPV)) 
b + geom_point(aes(color = Overlap)) + geom_hline(yintercept=0.50) + geom_vline(xintercept=0.50) + theme_bw() + theme(panel.grid.major=element_blank(), panel.grid.minor=element_blank()) +
  geom_text_repel(aes(label = .labs,  color = Overlap), size = 3, max.overlaps=Inf)+ scale_x_continuous(limits=c(0,1)) + scale_y_continuous(limits=c(0,1)) + 
  scale_color_manual(labels=c("1 base pair", "250kb", "500kb", "750kb"), values = c("red", "blue", "green", "purple", "black")) + ggtitle("SN vs PPV for Nominated Loci (+/-500kb), SCZ") + theme(plot.title=element_text(hjust=0.5)) + annotation_custom(grob1) + annotation_custom(grob2) + annotation_custom(grob3) + annotation_custom(grob4)
dev.off()

grob1 <- grobTree(textGrob("I", x=0.55, y=0.95, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob2 <- grobTree(textGrob("II", x=0.44, y=0.95, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob3 <- grobTree(textGrob("III", x=0.43, y=0.45, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob4 <- grobTree(textGrob("IV", x=0.55, y=0.45, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))

#Figure S3d 
ppi <- 300
png(filename="OUTPUT_PATH/FigureS3d.png", width=8, height=8, unit="in", res=ppi)
.labs <- mpv$Method4
b <- ggplot(mpv, aes(x = SN, y = PPV)) 
b + geom_point(aes(color = Overlap)) + geom_hline(yintercept=0.50) + geom_vline(xintercept=0.50) + theme_bw() + theme(panel.grid.major=element_blank(), panel.grid.minor=element_blank()) +
  geom_text_repel(aes(label = .labs,  color = Overlap), size = 3, max.overlaps=Inf)+ scale_x_continuous(limits=c(0,1)) + scale_y_continuous(limits=c(0,1)) + 
  scale_color_manual(labels=c("1 base pair", "250kb", "500kb", "750kb"), values = c("red", "blue", "green", "purple", "black")) + ggtitle("SN vs PPV for Nominated Loci (+/-500kb), MPV") + theme(plot.title=element_text(hjust=0.5)) + annotation_custom(grob1) + annotation_custom(grob2) + annotation_custom(grob3) + annotation_custom(grob4)

dev.off()


grob1 <- grobTree(textGrob("I", x=0.55, y=0.95, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob2 <- grobTree(textGrob("II", x=0.44, y=0.95, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob3 <- grobTree(textGrob("III", x=0.43, y=0.05, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))
grob4 <- grobTree(textGrob("IV", x=0.55, y=0.05, hjust=0, gp=gpar(col="black", fontsize=13, fontface="bold")))


#Figure S3e 
ppi <- 300
png(filename="OUTPUT_PATH/FigureS3e.png", width=8, height=8, unit="in", res=ppi)
.labs <- wbc$Method4
b <- ggplot(wbc, aes(x = SN, y = PPV)) 
b + geom_point(aes(color = Overlap)) + geom_hline(yintercept=0.50) + geom_vline(xintercept=0.50) + theme_bw() + theme(panel.grid.major=element_blank(), panel.grid.minor=element_blank()) +
  geom_text_repel(aes(label = .labs,  color = Overlap), size = 3, max.overlaps=Inf)+ scale_x_continuous(limits=c(0,1)) + scale_y_continuous(limits=c(0,1)) + 
  scale_color_manual(labels=c("1 base pair", "250kb", "500kb", "750kb"), values = c("red", "blue", "green", "purple", "black")) + ggtitle("SN vs PPV for Nominated Loci (+/-500kb), WBC") + theme(plot.title=element_text(hjust=0.5)) + annotation_custom(grob1) + annotation_custom(grob2) + annotation_custom(grob3) + annotation_custom(grob4)


dev.off()