diff --git a/notebooks/04_genetic_load.qmd b/notebooks/04_genetic_load.qmd index 026e375..c3eea9c 100644 --- a/notebooks/04_genetic_load.qmd +++ b/notebooks/04_genetic_load.qmd @@ -122,7 +122,7 @@ gerp <- ggplot(gerp_all, aes(x = time, y = relload * 1000)) + position = position_jitterdodge(jitter.width = 0.05) ) + scale_color_gradient(high = "#6e016b", low = "#9ebcda") + - ylab("Conserved Regions") + + ylab("Relative derived allele
count (conserved pos)") + scale_y_continuous(expand = expansion(mult = c(0.05, 0.20))) + geom_pwc(hide.ns = TRUE, label = "p.signif", method = "t.test") + theme_bw() + @@ -141,7 +141,6 @@ gerp_hom <- ggplot(gerp_all, aes(x = time, y = relload_hom * 1000)) + position = position_jitterdodge(jitter.width = 0.05) ) + scale_color_gradient(high = "#6e016b", low = "#9ebcda") + - ylab("Conserved Regions") + scale_y_continuous(expand = expansion(mult = c(0.05, 0.20))) + geom_pwc(hide.ns = TRUE, label = "p.signif", method = "t.test") + theme_bw() + @@ -160,11 +159,15 @@ gerp_stats <- gerp_all %>% group_by(species) %>% summarise( method = t.test(relload * 1000 ~ time)$method, + meanmod = t.test(relload * 1000 ~ time)$estimate[1], + meanhist = t.test(relload * 1000 ~ time)$estimate[2], meandiff = t.test(relload * 1000 ~ time)$estimate[1] - t.test(relload * 1000 ~ time)$estimate[2], conf.low = t.test(relload * 1000 ~ time)$conf.int[1], conf.hi = t.test(relload * 1000 ~ time)$conf.int[2], stat = t.test(relload * 1000 ~ time)$statistic, p.value = t.test(relload * 1000 ~ time)$p.value, + meanmod_rel = t.test(relload_hom * 1000 ~ time)$estimate[1], + meanhist_rel = t.test(relload_hom * 1000 ~ time)$estimate[2], meandiff_rel = t.test(relload_hom * 1000 ~ time)$estimate[1] - t.test(relload_hom * 1000 ~ time)$estimate[2], conf.low_rel = t.test(relload_hom * 1000 ~ time)$conf.int[1], conf.hi_rel = t.test(relload_hom * 1000 ~ time)$conf.int[2], @@ -264,7 +267,7 @@ high <- ggplot(varcounts_all, aes(x = time, y = high * 1000 / alts)) + position = position_jitterdodge(jitter.width = 0.05) ) + scale_color_gradient(high = "#6e016b", low = "#9ebcda") + - ylab("High Impact") + + ylab("Relative LoF
allele count") + scale_y_continuous(expand = expansion(mult = c(0.05, 0.20))) + geom_pwc(hide.ns = TRUE, label = "p.signif", method = "t.test") + theme_bw() + @@ -283,13 +286,13 @@ high_hom <- ggplot(varcounts_all, aes(x = time, y = high_hom * 1000 / alts)) + position = position_jitterdodge(jitter.width = 0.05) ) + scale_color_gradient(high = "#6e016b", low = "#9ebcda") + - ylab("High Impact") + - scale_y_continuous(expand = expansion(mult = c(0.05, 0.20))) + + ylim(c(0.13, 0.5)) + geom_pwc(hide.ns = TRUE, label = "p.signif", method = "t.test") + theme_bw() + theme( panel.grid.major = element_blank(), panel.grid.minor = element_blank(), + axis.title.y = element_blank(), axis.title.x = element_blank(), strip.text.x = element_text(size = 10, face = "italic") ) @@ -302,7 +305,7 @@ mod <- ggplot(varcounts_all, aes(x = time, y = mod * 1000 / alts)) + position = position_jitterdodge(jitter.width = 0.05) ) + scale_color_gradient(high = "#6e016b", low = "#9ebcda") + - ylab("Moderate Impact") + + ylab("Relative missense
allele count") + scale_y_continuous(expand = expansion(mult = c(0.05, 0.20))) + geom_pwc(hide.ns = TRUE, label = "p.signif", method = "t.test") + theme_bw() + @@ -321,13 +324,13 @@ mod_hom <- ggplot(varcounts_all, aes(x = time, y = mod_hom * 1000 / alts)) + position = position_jitterdodge(jitter.width = 0.05) ) + scale_color_gradient(high = "#6e016b", low = "#9ebcda") + - ylab("Moderate Impact") + scale_y_continuous(expand = expansion(mult = c(0.05, 0.20))) + geom_pwc(hide.ns = TRUE, label = "p.signif", method = "t.test") + theme_bw() + theme( panel.grid.major = element_blank(), panel.grid.minor = element_blank(), + axis.title.y = element_blank(), axis.title.x = element_blank(), strip.text.x = element_text(size = 10, face = "italic") ) @@ -340,11 +343,15 @@ mod_stats <- varcounts_all %>% group_by(species) %>% summarise( method = t.test(mod * 1000 / alts ~ time)$method, + meanmod = t.test(mod * 1000 / alts ~ time)$estimate[1], + meanhist = t.test(mod * 1000 / alts ~ time)$estimate[2], meandiff = t.test(mod * 1000 / alts ~ time)$estimate[1] - t.test(mod * 1000 / alts ~ time)$estimate[2], conf.low = t.test(mod * 1000 / alts ~ time)$conf.int[1], conf.hi = t.test(mod * 1000 / alts ~ time)$conf.int[2], stat = t.test(mod * 1000 / alts ~ time)$statistic, p.value = t.test(mod * 1000 / alts ~ time)$p.value, + meanmod_rel = t.test(mod_hom * 1000 / alts ~ time)$estimate[1], + meanhist_rel = t.test(mod_hom * 1000 / alts ~ time)$estimate[2], meandiff_rel = t.test(mod_hom * 1000 / alts ~ time)$estimate[1] - t.test(mod_hom * 1000 / alts ~ time)$estimate[2], conf.low_rel = t.test(mod_hom * 1000 / alts ~ time)$conf.int[1], conf.hi_rel = t.test(mod_hom * 1000 / alts ~ time)$conf.int[2], @@ -356,11 +363,15 @@ high_stats <- varcounts_all %>% group_by(species) %>% summarise( method = t.test(high * 1000 / alts ~ time)$method, + meanmod = t.test(high * 1000 / alts ~ time)$estimate[1], + meanhist = t.test(high * 1000 / alts ~ time)$estimate[2], meandiff = t.test(high * 1000 / alts ~ time)$estimate[1] - t.test(high * 1000 / alts ~ time)$estimate[2], conf.low = t.test(high * 1000 / alts ~ time)$conf.int[1], conf.hi = t.test(high * 1000 / alts ~ time)$conf.int[2], stat = t.test(high * 1000 / alts ~ time)$statistic, p.value = t.test(high * 1000 / alts ~ time)$p.value, + meanmod_rel = t.test(high_hom * 1000 / alts ~ time)$estimate[1], + meanhist_rel = t.test(high_hom * 1000 / alts ~ time)$estimate[2], meandiff_rel = t.test(high_hom * 1000 / alts ~ time)$estimate[1] - t.test(high_hom * 1000 / alts ~ time)$estimate[2], conf.low_rel = t.test(high_hom * 1000 / alts ~ time)$conf.int[1], conf.hi_rel = t.test(high_hom * 1000 / alts ~ time)$conf.int[2], @@ -532,12 +543,12 @@ figures depicting genetic load. #| fig-height: 8 #| fig-width: 8 -gerp_clean <- gerp + - ggtitle("Total Genetic Load") + +mod_clean <- mod + + ggtitle("Total Deleterious Burden") + theme( plot.margin = unit(c(5.5, 5.5, 3, 5.5), "pt"), legend.position = "none", - axis.title.y = element_text(size = 10), + axis.title.y = element_markdown(size = 8), axis.text.x = element_blank(), strip.background = element_blank() ) @@ -547,28 +558,28 @@ high_clean <- high + plot.margin = unit(c(3, 5.5, 3, 5.5), "pt"), legend.position = "none", strip = element_blank(), - axis.title.y = element_text(size = 10), + axis.title.y = element_markdown(size = 8), axis.text.x = element_blank(), strip.text.x = element_blank(), strip.background = element_blank() ) -mod_clean <- mod + +gerp_clean <- gerp + theme( plot.margin = unit(c(3, 5.5, 5.5, 5.5), "pt"), legend.position = "none", strip = element_blank(), - axis.title.y = element_text(size = 10), + axis.title.y = element_markdown(size = 8), strip.text.x = element_blank(), strip.background = element_blank() ) -gerp_hom_clean <- gerp_hom + - ggtitle("Realized Genetic Load") + +mod_hom_clean <- mod_hom + + ggtitle("Homozygous Deleterious Burden") + theme( plot.margin = unit(c(5.5, 5.5, 3, 5.5), "pt"), legend.position = "none", - axis.title.y = element_text(size = 10), + axis.title.y = element_blank(), axis.text.x = element_blank(), strip.background = element_blank() ) @@ -578,41 +589,41 @@ high_hom_clean <- high_hom + plot.margin = unit(c(3, 5.5, 3, 5.5), "pt"), legend.position = "none", strip = element_blank(), - axis.title.y = element_text(size = 10), + axis.title.y = element_blank(), axis.text.x = element_blank(), strip.text.x = element_blank(), strip.background = element_blank() ) -mod_hom_clean <- mod_hom + +gerp_hom_clean <- gerp_hom + theme( plot.margin = unit(c(3, 5.5, 5.5, 5.5), "pt"), legend.position = "none", strip = element_blank(), - axis.title.y = element_text(size = 10), + axis.title.y = element_blank(), strip.text.x = element_blank(), strip.background = element_blank() ) total_load <- plot_grid( - gerp_clean, - high_clean, mod_clean, + high_clean, + gerp_clean, rel_heights = c(1.2, 0.9, 1), ncol = 1, align = "v" ) real_load <- plot_grid( - gerp_hom_clean, - high_hom_clean, mod_hom_clean, + high_hom_clean, + gerp_hom_clean, rel_heights = c(1.2, 0.9, 1), ncol = 1, align = "v" ) -load <- plot_grid(total_load, real_load, ncol = 2, labels = c("B", "C")) +load <- plot_grid(total_load, real_load, ncol = 2, labels = c("B", "C"), rel_widths = c(1.1, 1)) legend_inb <- get_plot_component( gerp + @@ -652,7 +663,7 @@ gerpreg <- ggplot(gerp_csemi, aes(x = Froh, y = relload)) + geom_point(aes(y = relload_hom), color = "blue") + geom_smooth(method = "lm", color = "red") + geom_smooth(aes(y = relload_hom), method = "lm", color = "blue") + - ylab("Genetic Load") + + ylab("Relative count deleterious mutations") + xlab("Inbreeding Coefficient (*F~RoH~*)") + stat_cor(color = "red", label.y = 0.4) + stat_cor(aes(y = relload_hom), color = "blue", label.y = 0.33) + @@ -668,7 +679,7 @@ highreg <- ggplot(var_csemi, aes(x = Froh, y = high / alts)) + geom_point(aes(y = high_hom / alts), color = "blue") + geom_smooth(method = "lm", color = "red") + geom_smooth(aes(y = high_hom / alts), method = "lm", color = "blue") + - ylab("Genetic Load") + + ylab("Relative count deleterious mutations") + xlab("Inbreeding Coefficient (*F~RoH~*)") + stat_cor(color = "red", label.y = 0.0011) + stat_cor(aes(y = high_hom / alts), label.y = 0, color = "blue") + @@ -684,7 +695,7 @@ modreg <- ggplot(var_csemi, aes(x = Froh, y = mod / alts)) + geom_point(aes(y = mod_hom / alts), color = "blue") + geom_smooth(method = "lm", color = "red") + geom_smooth(aes(y = mod_hom / alts), method = "lm", color = "blue") + - ylab("Genetic Load") + + ylab("Relative count deleterious mutations") + xlab("Inbreeding Coefficient (*F~RoH~*)") + stat_cor(color = "red", label.y = 0.05) + stat_cor(aes(y = mod_hom / alts), label.y = 0, color = "blue") +