p = h2_data %>%

# filter(qcflags.in_bounds_h2) %>%

filter(qcflags.pass_all) %>%

mutate(ancestry=fct_relevel(ancestry, pops_by_sample_size)) %>%

group_by(ancestry, trait_type) %>%

summarize(mean_observed_h2=mean(estimates.final.h2_observed, na.rm=T),

sd_observed_h2=sd(estimates.final.h2_observed, na.rm=T)) %>%

mutate(trait_type=fct_reorder(trait_type, -mean_observed_h2)) %>%

ggplot aes(x = ancestry, fill = trait_type, color = trait_type, y = mean_observed_h2)

# geom_bar(stat='identity', position='dodge')

geom_pointrange(position=position_dodge(width=0.75),

mapping=aes(ymin=mean_observed_h2-sd_observed_h2,

ymax=mean_observed_h2 sd_observed_h2))

trait_fill_scale trait_color_scale xlab(NULL)

scale_y_continuous(labels=percent, name=expression(paste('Mean observed ', h^2)))

theme(legend.position=c(0.01, 1), legend.justification=c(0, 1),

legend.background=element_rect(fill = alpha("white", 0)))

p

return(p)

high_level = 8

h2_plot_data = h2_data %>%

filter(qcflags.in_bounds_h2 & qcflags.normal_lambda & qcflags.normal_ratio) %>%

mutate(z=if_else(estimates.final.h2_z > high_level, high_level, estimates.final.h2_z)) %>%

filter(z > 0) %>%

mutate(ancestry=fct_relevel(ancestry, pops_by_sample_size))

h2_medians = h2_plot_data %>%

group_by(ancestry, trait_type) %>%

summarize(median_z=median(z))

colors_darker = darken(ukb_pop_colors, amount=0.375)

names(colors_darker) = names(ukb_pop_colors)

p = h2_plot_data %>%

ggplot aes(x = z, fill = ancestry)

geom_histogram() geom_vline(xintercept=4, linetype='dashed')

geom_vline(aes(xintercept = median_z, color=ancestry), data=h2_medians, linetype='dotted')

coord_cartesian(ylim=c(NA, 250))

scale_y_continuous(breaks=c(0, 125, 250))

# scale_x_continuous(breaks=c(0, 10, 20))

scale_x_continuous(breaks=c(0, 4, 8))

pop_fill_scale scale_color_manual(values=colors_darker)

facet_grid(rows=vars(ancestry), cols=vars(trait_type))

theme(strip.background = element_blank())

guides(fill=F, color=F) ylab('Number of phenotypes') xlab('Heritability z')

return(p)

output_type(output_format, paste0('extended_data_figure3.', output_format), height=8.5, width=5.5)

print(ggarrange(p1, p2, nrow = 2, labels='auto'))

dev.off()