vignettes/articles/plot_TAG_chain_length_vs_logFC.Rmd
plot_TAG_chain_length_vs_logFC.RmdThis article generates plots of triacylglycerol (TAG) chain length or number of double bonds vs. log\(_2\) fold-change (Extended Data Fig. 7B, C).
# Required packages
library(MotrpacRatTraining6moWATData)
library(dplyr)
library(ggplot2)
library(patchwork)
library(grid)
library(gridExtra)
library(lemon) # facet_rep_grid
library(latex2exp)
plot_TAG <- function(x) {
lapply(c("chain_length", "double_bond"), function(var_i) {
if (var_i == "chain_length") {
y_lims <- c(-1.5, 2)
x_minor_breaks <- seq(30, 60, 5)
x_breaks <- seq(30, 60, 10)
} else {
y_lims <- c(-1.4, 1.4)
x_minor_breaks <- 0:11
x_breaks <- seq(0, 11, 2)
}
ggplot(x, aes(x = !!sym(var_i),
y = logFC, color = sex)) +
geom_hline(color = "black", yintercept = 0, lty = "dashed",
linewidth = 0.3 * scale) +
geom_point(size = 1.2, alpha = 0.5) +
geom_smooth(linewidth = 0.4, se = TRUE, method = "loess",
span = 1, fill = "black", alpha = 0.2) +
# redraw lines on top
geom_smooth(linewidth = 0.3 * scale, se = FALSE, method = "loess",
span = 1, fill = "black", color = "black") +
lemon::facet_rep_grid(sex ~ timepoint, scales = "free_x",
repeat.tick.labels = "bottom") +
scale_y_continuous(name = latex2exp::TeX("log$_2$(fold-change)"),
expand = expansion(mult = 5e-3)) +
coord_cartesian(ylim = y_lims) +
scale_x_continuous(breaks = x_breaks,
minor_breaks = x_minor_breaks,
expand = expansion(5e-3)) +
scale_color_manual(name = NULL, values = c("#ff6eff", "#5555ff")) +
theme_bw() +
theme(text = element_text(size = 6.5 * scale, color = "black"),
line = element_line(linewidth = 0.3 * scale, color = "black"),
axis.line.y.right = element_blank(),
axis.ticks = element_line(linewidth = 0.3 * scale,
color = "black"),
axis.text = element_text(size = 5 * scale, color = "black"),
axis.title = element_text(size = 6.5 * scale, color = "black"),
axis.title.x = element_text(margin = margin(t = 6, unit = "pt")),
axis.title.y = element_text(margin = margin(r = 6, unit = "pt")),
strip.background = element_blank(),
strip.text = element_text(size = 6.5 * scale, hjust = 0),
panel.spacing.x = unit(ifelse(var_i == "chain_length",
0, -7 * scale), "pt"),
panel.grid.minor = element_blank(),
panel.grid = element_line(linewidth = 0.3 * scale),
strip.text.y = element_text(hjust = 0.5),
plot.title = element_text(size = 7 * scale, color = "black"),
plot.subtitle = element_text(size = 5.5 * scale, color = "black"))
})
}
x <- METAB_DA$trained_vs_SED %>%
filter(lipid_class == "TG") %>%
select(contrast, logFC, chain_length, double_bond) %>%
mutate(sex = substr(contrast, 1, 1),
sex = factor(sex, levels = c("F", "M"),
labels = c("Female", "Male")),
timepoint = gsub("[MF]_", "", contrast),
timepoint = factor(timepoint))
scale <- 2 # divide plot dimensions by 2 when adding to final figures.
plotlist <- plot_TAG(x)
plotlist[[1]] <- plotlist[[1]] +
labs(x = "TAG Chain Length") +
theme(panel.grid.minor.y = element_blank())
plotlist[[2]] <- plotlist[[2]] +
labs(x = "TAG Double Bonds")