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17_lipgmim_angptl4region.R
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17_lipgmim_angptl4region.R
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# Endothelial lipase (EL, LIPG) activity vs. ANGPTL4 region plot
library(data.table)
library(ggplot2)
# Get lipg mimicry data ----
ssi.lipg.angptl4 <- data.table::fread(file = "./data/ssi_lipg_angptl4.txt")
ssi.lipg.angptl4 <- ssi.lipg.angptl4[rsid != ".", ]
# Get ld matrix ----
# ldm <- ieugwasr::ld_matrix(ssi_angptl4$rsid, with_alleles = FALSE, pop = "EUR")
#data.table::fwrite(as.data.frame(ldm), file = "/Users/fredriklandfors/projekt/lipase_genmimicry/data/lipg/angptl4_ldm.txt", sep = "\t")
ldm <- data.table::fread(file = "/Users/fredriklandfors/projekt/lipase_genmimicry/data/angptl4/angptl4_ldm.txt")
ldm <- as.matrix(ldm)
ldm_2 <- ldm^2
ldm_2 <- data.frame(ldm_2)
ldm_3 <- ldm_2["rs116843064"]
ldm_4 <- data.frame(
rsid = colnames(ldm_2),
ld.rs116843064 = ldm_3$rs116843064
)
# Make plot df ----
plot_df <- merge(
ssi.lipg.angptl4,
ldm_4,
by = "rsid",
all.x = TRUE
)
plot_df$r2.ssi = plot_df$r2.ssi * 100
plot_df$rs116843064 <- ifelse(plot_df$rsid == "rs116843064", "rs116843064-A", "")
plot_df$E40K <- ifelse(plot_df$rsid == "rs116843064", TRUE, FALSE)
## Scatter plot: R2 vs. pos ----
p1 <- ggplot(data = plot_df, aes(x = pos.ssi, y = r2.ssi)) +
ggtitle("Endothelial lipase (EL, LIPG) activity R\U00B2 of variants in the ANGPTL4 region (19:8,229,011-8,629,011)") +
ylab("Explained LIPG activity [rs77960347-G] (R\U00B2 %)") +
xlab("Chromosomal position (base pairs)") +
geom_point(aes(color = ld.rs116843064, shape = E40K)) +
geom_text(aes(label = rs116843064), vjust = 0.25, hjust = -0.1,
family = "Helvetica", colour = "black", fontface = "bold", size = 2.5) +
scale_y_continuous(limits = c(0, 100), breaks = seq(0, 100, 10)) +
scale_x_continuous(
breaks = seq(8300000, 8600000, 100000),
limits = c(8229011, 8629011),
labels = c("8,300,000", "8,400,000", "8,500,000", "8,600,000")
) +
scale_color_gradientn(
colors = c("#00008b", "#87ceeb", "#006400", "#ffa500", "#FF0000"),
name = "LD (r\U00B2)",
n.breaks = 6
) +
theme_classic() +
theme(
plot.title = element_text(family = "Helvetica", hjust = 0.5, size = 10,
colour = "black", face = "bold"),
axis.text = element_text(family = "Helvetica", colour = "black", face = "plain", size = 8),
axis.ticks = element_line(colour = "black"),
axis.title = element_text(family = "Helvetica", colour = "black", face = "bold", size = 8)
)
# Write to file
ggsave(plot = p1,
path = "/Users/fredriklandfors/projekt/lipase_genmimicry/plots/sensitivity/lipg_angptl4/",
filename = "lipg_angptl4.pdf",
width = 5*1.5, height = 5, units = "in",
dpi = 1100)
## Gene tracks plot ----
library(ggbio)
library(Homo.sapiens)
x1 <- "chr19:8229011-8629011"
x2 <- as(x1, "GRanges")
class(Homo.sapiens)
p.txdb <- autoplot(Homo.sapiens, which = x2,
# stat = "reduce",
rownames.label = TRUE,
label.size = 1.5,
label.color = "black")
# Write to file
pdf(
file = "/Users/fredriklandfors/projekt/lipase_genmimicry/plots/sensitivity/lipg_angptl4/lipga4_organismdb_track.pdf",
width = 5*1.5 * 0.7945,
height = 2
)
p.txdb +
theme_classic(
) +
scale_x_continuous(
breaks = seq(8300000, 8600000, 100000),
limits = c(8229011, 8629011),
#labels = c("8.3 Mb", "8.4 Mb", "8.5 Mb", "8.6 Mb"),
labels = c("", "", "", "")
)
dev.off()
## end ----