Figure 4a. Variant set -level Excess-of-overlap (EOO) analysis.

Variant set -level Excess-of-overlap (EOO) analysis of (i) 95% CoS-gene links from xQTL-only ColocBoost, (ii) standard marginal xQTL-gene associations, merged across all 17 xQTL datasets (Methods) and (iii) 95% credible set (CS)-gene links from SuSIE finemapping, merged across all 17 xQTL datasets (Methods), against 569 silver-standard element-gene links from 3 aggregated CRISPR interference (CRISPRi) datasets in K562 cell line using KRAB-dCas9 protocol, and 8,192 silver-standard element-gene links from the recent STING-seq data in K562 using a newer KRAB-dCas9-MeCP2 protocol.

library(ggplot2)
library(ggsci)
library(ggpattern)
data <- readRDS("Figure_4a_Variant_EOO.rds")
sdtimes <- 1.96
p1 <- ggplot(data, aes(x = method, y = enrichment, fill = method, pattern = cate)) +
  geom_bar_pattern(
    aes(pattern = cate),
    stat = "identity",
    position = position_dodge(width = 0.7),
    width = 0.7,
    color = "black", # Solid border
    pattern_fill = "grey40", # Pattern color
    pattern_angle = 45, # Angle of the dashed line
    pattern_density = 0.05, # Spacing of the dashed line
    pattern_spacing = 0.05 # Line spacing
  ) +
  geom_text(
    data = subset(data, P <= 0.05/3 & enrichment > 0),
    aes(label = "*", y = enrichment + sdtimes * sd + 0.03, group = cate),
    vjust = 0, color = "#F94144", size = 10, position = position_dodge(0.7)
  ) +
  scale_pattern_manual(values = c("none", "stripe")) +
  geom_errorbar(aes(ymin = enrichment - sdtimes*sd, ymax = enrichment + sdtimes*sd), width = 0.2, position = position_dodge(0.7), linewidth = 1) +
  geom_hline(yintercept = 1, linetype = "dashed", color = "grey20", linewidth = 1)  + 
  scale_fill_brewer(palette = "Set1") +
  labs(
    title = "",
    x = "",
    y = "Enrichment\n(variant-gene concordant links)"
  ) +
  ylim(c(0,25)) +
  theme_minimal(base_size = 15) +
  theme(
    plot.title = element_text(size = 0, face = "bold", hjust = 0.5),
    axis.title.x = element_text(size = 0),
    axis.title.y = element_text(size = 24),
    axis.text.y = element_text(size = 20, margin = margin(r = 0), angle = 90, hjust = 0.5, vjust = 0),
    axis.text.x = element_text(size = 20, margin = margin(t = 0)),
    legend.position = "inside",
    legend.justification = c(0.9, 0.9),
    legend.title = element_text(size = 0),
    legend.text = element_text(size = 20),
    legend.spacing.y = unit(1.5, "cm"),
    panel.border = element_rect(color = "grey20", fill = NA, linewidth = 1.5),
    panel.grid.major = element_blank(),      # Remove major grid lines
    panel.grid.minor = element_blank(),      # Remove minor grid lines
  ) +
  guides(fill = "none",
         pattern = guide_legend(
           override.aes = list(
             fill = c("white", "lightgrey"),  # Adjust background color for the legend
             color = "black"                 # Keep border color
           )
         )
  )

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