Figure 6a. UpSet plot comparison.

UpSet plot of distinct (i) 95% CoS identified by GWAS–xQTL ColocBoost, (ii) union of 95% CoS identified via applying COLOC on each xQTL with AD GWAS (COLOC-union), and (iii) 95% SuSiE credible sets (CS) from AD GWAS fine‐mapping.

library("UpSetR")
data <- readRDS("Figure_6a.rds")
comparison <- apply(data, 2, which)
names(comparison) <- c("AD Fine-mapping", "ColocBoost", "COLOC (V5)")
max_size <- max(sapply(comparison, length))
p1 <- upset(fromList(comparison), 
            order.by = "freq", 
            keep.order = T,
            main.bar.color = "steelblue3", 
            sets.bar.color = "sandybrown", 
            text.scale = c(2,2,3,2,2,2.3), # Adjust font sizes for the main title, set names, set sizes, intersection sizes, and axis titles
            matrix.color = "black", # Adjust the color of matrix dots
            number.angles = 0, # Adjust the angle of number labels, useful for some plots
            mb.ratio = c(0.5, 0.5), # Adjust the ratio of main bar and sets bar
            point.size = 6, line.size = 1.5,
            sets = c("COLOC (V5)", "AD Fine-mapping", "ColocBoost"),  
            nsets = length(coloc),
            set_size.show = TRUE,
            set_size.angles = 0,
            set_size.numbers_size = 7,
            set_size.scale_max = max_size + 0.25*max_size,
            nintersects = 25,
            mainbar.y.label = "",
            sets.x.label = NULL)

options(repr.plot.width = 10, repr.plot.height = 8)
p1