Volcano_plots_journal.R

main_dir <- dirname(rstudioapi::getSourceEditorContext()$path)
setwd(main_dir)

if (!require("pacman"))
  install.packages("pacman")

pacman::p_load(tidyverse, ggtext, ggrepel)

#####################
###### SPECIES ######
#####################

DAA_species <- read.csv("MaAsLin2_results/species/all_results.tsv", sep = "\t")

DAA_species$diffabund <- "NO"
DAA_species$diffabund[DAA_species$coef > 1 &
                        DAA_species$qval < 0.05 &
                        DAA_species$metadata == "Group"] <- "NN_plus"
DAA_species$diffabund[DAA_species$coef < -1 &
                        DAA_species$qval < 0.05 &
                        DAA_species$metadata == "Group"] <- "NN_minus"
DAA_species$feature[DAA_species$diffabund == "NO"] <- NA
DAA_species$label <- NA
top_red <- DAA_species[DAA_species$coef < -1 &
                         DAA_species$qval < 0.05 & DAA_species$metadata == "Group", ]
top_red <- top_red[order(top_red$qval), ][1:5, ]
DAA_species$label[DAA_species$feature %in% top_red$feature] <- DAA_species$feature[DAA_species$feature %in% top_red$feature]
DAA_species$label[DAA_species$coef > 1 &
                    DAA_species$qval < 0.05 &
                    DAA_species$metadata == "Group"] <- DAA_species$feature[DAA_species$coef > 1 &
                                                                              DAA_species$qval < 0.05 & DAA_species$metadata == "Group"]

volcano_plot_species <- ggplot(data = DAA_species, aes(
  x = coef,
  y = -log10(qval),
  label = feature,
  col = diffabund
)) +
  geom_point(size = 2) +
  theme_bw() +
  geom_vline(xintercept = c(-1, 1),
             col = "gray",
             linetype = 'dashed') +
  geom_hline(
    yintercept = c(-log10(0.05)),
    col = "gray",
    linetype = 'dashed'
  ) +
  geom_text_repel(
    data = subset(DAA_species, !is.na(label)),
    aes(label = label),
    size = 2,
    box.padding = 1,
    point.padding = 0.5,
    max.overlaps = 10,
    nudge_x = 2,
    nudge_y = 3,
    force = 10
  ) +
  scale_color_manual(
    name = NULL,
    values = c("grey"),
    labels = c("<strong>Not significant:</strong><br>q-value>0.05")
  ) +
  labs(x = "Log2fc") +
  theme(
    plot.title = element_text(size = 22),
    legend.text = element_markdown(size = 14),
    plot.caption = element_text(size = 22),
    axis.text = element_text(size = 14),
    axis.title = element_text(size = 16, vjust = 0)
  ) +
  guides(colour = guide_legend(override.aes = list(size = 3.5)))

ggsave(
  "images/volcano_plots/volcano_plot_species.png",
  plot = volcano_plot_species,
  width = 10,
  height = 6,
  dpi = 600
)


###################
###### GENUS ######
###################

DAA_genus <- read.csv("MaAsLin2_results/genus/all_results.tsv", sep = "\t")

DAA_genus$diffabund <- "NO"
DAA_genus$diffabund[DAA_genus$coef > 1 &
                      DAA_genus$qval < 0.05 & DAA_genus$metadata == "Group"] <- "NN_plus"
DAA_genus$diffabund[DAA_genus$coef < -1 &
                      DAA_genus$qval < 0.05 &
                      DAA_genus$metadata == "Group"] <- "NN_minus"
DAA_genus$feature[DAA_genus$diffabund == "NO"] <- NA
DAA_genus$label <- NA
top_red <- DAA_genus[DAA_genus$coef < -1 &
                       DAA_genus$qval < 0.05 & DAA_genus$metadata == "Group", ]
top_red <- top_red[order(top_red$qval), ][1:5, ]
DAA_genus$label[DAA_genus$feature %in% top_red$feature] <- DAA_genus$feature[DAA_genus$feature %in% top_red$feature]
DAA_genus$label[DAA_genus$coef > 1 &
                  DAA_genus$qval < 0.05 &
                  DAA_genus$metadata == "Group"] <- DAA_genus$feature[DAA_genus$coef > 1 &
                                                                        DAA_genus$qval < 0.05 & DAA_genus$metadata == "Group"]

volcano_plot_genus <- ggplot(data = DAA_genus, aes(
  x = coef,
  y = -log10(qval),
  label = feature,
  col = diffabund
)) +
  geom_point(size = 2) +
  theme_bw() +
  geom_vline(xintercept = c(-1, 1),
             col = "gray",
             linetype = 'dashed') +
  geom_hline(
    yintercept = c(-log10(0.05)),
    col = "gray",
    linetype = 'dashed'
  ) +
  geom_text_repel(
    data = subset(DAA_species, !is.na(label)),
    aes(label = label),
    size = 2,
    box.padding = 1,
    point.padding = 0.5,
    max.overlaps = 10,
    nudge_x = 2,
    nudge_y = 3,
    force = 10
  ) +
  scale_color_manual(
    name = NULL,
    values = c("grey"),
    labels = c("<strong>Not significant:</strong><br>q-value>0.05")
  ) +
  labs(x = "Log2fc") +
  theme(
    plot.title = element_text(size = 22),
    legend.text = element_markdown(size = 14),
    plot.caption = element_text(size = 22),
    axis.text = element_text(size = 14),
    axis.title = element_text(size = 16, vjust = 0)
  ) +
  guides(colour = guide_legend(override.aes = list(size = 3.5)))

ggsave(
  "images/volcano_plots/volcano_plot_genus.png",
  plot = volcano_plot_genus,
  width = 10,
  height = 6,
  dpi = 600
)


####################
###### FAMILY ######
####################

DAA_family <- read.csv("MaAsLin2_results/family/all_results.tsv", sep = "\t")

DAA_family$diffabund <- "NO"
DAA_family$diffabund[DAA_family$coef > 1 &
                       DAA_family$qval < 0.05 &
                       DAA_family$metadata == "Group"] <- "NN_plus"
DAA_family$diffabund[DAA_family$coef < -1 &
                       DAA_family$qval < 0.05 &
                       DAA_family$metadata == "Group"] <- "NN_minus"
DAA_family$feature[DAA_family$diffabund == "NO"] <- NA
DAA_family$label <- NA
top_red <- DAA_family[DAA_family$coef < -1 &
                        DAA_family$qval < 0.05 & DAA_family$metadata == "Group", ]
top_red <- top_red[order(top_red$qval), ][1:5, ]
DAA_family$label[DAA_family$feature %in% top_red$feature] <- DAA_family$feature[DAA_family$feature %in% top_red$feature]
DAA_family$label[DAA_family$coef > 1 &
                   DAA_family$qval < 0.05 &
                   DAA_family$metadata == "Group"] <- DAA_family$feature[DAA_family$coef > 1 &
                                                                           DAA_family$qval < 0.05 & DAA_family$metadata == "Group"]

volcano_plot_family <- ggplot(data = DAA_family, aes(
  x = coef,
  y = -log10(qval),
  label = feature,
  col = diffabund
)) +
  geom_point(size = 2) +
  theme_bw() +
  geom_vline(xintercept = c(-1, 1),
             col = "gray",
             linetype = 'dashed') +
  geom_hline(
    yintercept = c(-log10(0.05)),
    col = "gray",
    linetype = 'dashed'
  ) +
  geom_text_repel(
    data = subset(DAA_species, !is.na(label)),
    aes(label = label),
    size = 2,
    box.padding = 1,
    point.padding = 0.5,
    max.overlaps = 10,
    nudge_x = 2,
    nudge_y = 3,
    force = 10
  ) +
  scale_color_manual(
    name = NULL,
    values = c("grey"),
    labels = c("<strong>Not significant:</strong><br>q-value>0.05")
  ) +
  labs(x = "Log2fc") +
  theme(
    plot.title = element_text(size = 22),
    legend.text = element_markdown(size = 14),
    plot.caption = element_text(size = 22),
    axis.text = element_text(size = 14),
    axis.title = element_text(size = 16, vjust = 0)
  ) +
  guides(colour = guide_legend(override.aes = list(size = 3.5)))

ggsave(
  "images/volcano_plots/volcano_plot_family.png",
  plot = volcano_plot_family,
  width = 10,
  height = 6,
  dpi = 600
)


###################
###### ORDER ######
###################

DAA_order <- read.csv("MaAsLin2_results/order/all_results.tsv", sep = "\t")

DAA_order$diffabund <- "NO"
DAA_order$diffabund[DAA_order$coef > 1 &
                      DAA_order$qval < 0.05 & DAA_order$metadata == "Group"] <- "NN_plus"
DAA_order$diffabund[DAA_order$coef < -1 &
                      DAA_order$qval < 0.05 &
                      DAA_order$metadata == "Group"] <- "NN_minus"
DAA_order$feature[DAA_order$diffabund == "NO"] <- NA
DAA_order$label <- NA
top_red <- DAA_order[DAA_order$coef < -1 &
                       DAA_order$qval < 0.05 & DAA_order$metadata == "Group", ]
top_red <- top_red[order(top_red$qval), ][1:5, ]
DAA_order$label[DAA_order$feature %in% top_red$feature] <- DAA_order$feature[DAA_order$feature %in% top_red$feature]
DAA_order$label[DAA_order$coef > 1 &
                  DAA_order$qval < 0.05 &
                  DAA_order$metadata == "Group"] <- DAA_order$feature[DAA_order$coef > 1 &
                                                                        DAA_order$qval < 0.05 & DAA_order$metadata == "Group"]

volcano_plot_order <- ggplot(data = DAA_order, aes(
  x = coef,
  y = -log10(qval),
  label = feature,
  col = diffabund
)) +
  geom_point(size = 2) +
  theme_bw() +
  geom_vline(xintercept = c(-1, 1),
             col = "gray",
             linetype = 'dashed') +
  geom_hline(
    yintercept = c(-log10(0.05)),
    col = "gray",
    linetype = 'dashed'
  ) +
  geom_text_repel(
    data = subset(DAA_species, !is.na(label)),
    aes(label = label),
    size = 2,
    box.padding = 1,
    point.padding = 0.5,
    max.overlaps = 10,
    nudge_x = 2,
    nudge_y = 3,
    force = 10
  ) +
  scale_color_manual(
    name = NULL,
    values = c("grey"),
    labels = c("<strong>Not significant:</strong><br>q-value>0.05")
  ) +
  labs(x = "Log2fc") +
  theme(
    plot.title = element_text(size = 22),
    legend.text = element_markdown(size = 14),
    plot.caption = element_text(size = 22),
    axis.text = element_text(size = 14),
    axis.title = element_text(size = 16, vjust = 0)
  ) +
  guides(colour = guide_legend(override.aes = list(size = 3.5)))

ggsave(
  "images/volcano_plots/volcano_plot_order.png",
  plot = volcano_plot_order,
  width = 10,
  height = 6,
  dpi = 600
)

###################
###### CLASS ######
###################

DAA_class <- read.csv("MaAsLin2_results/class/all_results.tsv", sep = "\t")

DAA_class$diffabund <- "NO"
DAA_class$diffabund[DAA_class$coef > 1 &
                      DAA_class$qval < 0.05 & DAA_class$metadata == "Group"] <- "NN_plus"
DAA_class$diffabund[DAA_class$coef < -1 &
                      DAA_class$qval < 0.05 &
                      DAA_class$metadata == "Group"] <- "NN_minus"
DAA_class$feature[DAA_class$diffabund == "NO"] <- NA
DAA_class$label <- NA
top_red <- DAA_class[DAA_class$coef < -1 &
                       DAA_class$qval < 0.05 & DAA_class$metadata == "Group", ]
top_red <- top_red[order(top_red$qval), ][1:5, ]
DAA_class$label[DAA_class$feature %in% top_red$feature] <- DAA_class$feature[DAA_class$feature %in% top_red$feature]
DAA_class$label[DAA_class$coef > 1 &
                  DAA_class$qval < 0.05 &
                  DAA_class$metadata == "Group"] <- DAA_class$feature[DAA_class$coef > 1 &
                                                                        DAA_class$qval < 0.05 & DAA_class$metadata == "Group"]

volcano_plot_class <- ggplot(data = DAA_class, aes(
  x = coef,
  y = -log10(qval),
  label = feature,
  col = diffabund
)) +
  geom_point(size = 2) +
  theme_bw() +
  geom_vline(xintercept = c(-1, 1),
             col = "gray",
             linetype = 'dashed') +
  geom_hline(
    yintercept = c(-log10(0.05)),
    col = "gray",
    linetype = 'dashed'
  ) +
  geom_text_repel(
    data = subset(DAA_species, !is.na(label)),
    aes(label = label),
    size = 2,
    box.padding = 1,
    point.padding = 0.5,
    max.overlaps = 10,
    nudge_x = 2,
    nudge_y = 3,
    force = 10
  ) +
  scale_color_manual(
    name = NULL,
    values = c("grey"),
    labels = c("<strong>Not significant:</strong><br>q-value>0.05")
  ) +
  labs(x = "Log2fc") +
  theme(
    plot.title = element_text(size = 22),
    legend.text = element_markdown(size = 14),
    plot.caption = element_text(size = 22),
    axis.text = element_text(size = 14),
    axis.title = element_text(size = 16, vjust = 0)
  ) +
  guides(colour = guide_legend(override.aes = list(size = 3.5)))

ggsave(
  "images/volcano_plots/volcano_plot_class.png",
  plot = volcano_plot_class,
  width = 10,
  height = 6,
  dpi = 600
)


####################
###### PHYLUM ######
####################

DAA_phylum <- read.csv("MaAsLin2_results/phylum/all_results.tsv", sep = "\t")

DAA_phylum$diffabund <- "NO"
DAA_phylum$diffabund[DAA_phylum$coef > 1 &
                       DAA_phylum$qval < 0.05 &
                       DAA_phylum$metadata == "Group"] <- "NN_plus"
DAA_phylum$diffabund[DAA_phylum$coef < -1 &
                       DAA_phylum$qval < 0.05 &
                       DAA_phylum$metadata == "Group"] <- "NN_minus"
DAA_phylum$feature[DAA_phylum$diffabund == "NO"] <- NA
DAA_phylum$label <- NA
top_red <- DAA_phylum[DAA_phylum$coef < -1 &
                        DAA_phylum$qval < 0.05 & DAA_phylum$metadata == "Group", ]
top_red <- top_red[order(top_red$qval), ][1:5, ]
DAA_phylum$label[DAA_phylum$feature %in% top_red$feature] <- DAA_phylum$feature[DAA_phylum$feature %in% top_red$feature]
DAA_phylum$label[DAA_phylum$coef > 1 &
                   DAA_phylum$qval < 0.05 &
                   DAA_phylum$metadata == "Group"] <- DAA_phylum$feature[DAA_phylum$coef > 1 &
                                                                           DAA_phylum$qval < 0.05 & DAA_phylum$metadata == "Group"]

volcano_plot_phylum <- ggplot(data = DAA_phylum, aes(
  x = coef,
  y = -log10(qval),
  label = feature,
  col = diffabund
)) +
  geom_point(size = 2) +
  theme_bw() +
  geom_vline(xintercept = c(-1, 1),
             col = "gray",
             linetype = 'dashed') +
  geom_hline(
    yintercept = c(-log10(0.05)),
    col = "gray",
    linetype = 'dashed'
  ) +
  geom_text_repel(
    data = subset(DAA_species, !is.na(label)),
    aes(label = label),
    size = 2,
    box.padding = 1,
    point.padding = 0.5,
    max.overlaps = 10,
    nudge_x = 2,
    nudge_y = 3,
    force = 10
  ) +
  scale_color_manual(
    name = NULL,
    values = c("grey"),
    labels = c("<strong>Not significant:</strong><br>q-value>0.05")
  ) +
  labs(x = "Log2fc") +
  theme(
    plot.title = element_text(size = 22),
    legend.text = element_markdown(size = 14),
    plot.caption = element_text(size = 22),
    axis.text = element_text(size = 14),
    axis.title = element_text(size = 16, vjust = 0)
  ) +
  guides(colour = guide_legend(override.aes = list(size = 3.5)))

ggsave(
  "images/volcano_plots/volcano_plot_phylum.png",
  plot = volcano_plot_phylum,
  width = 10,
  height = 6,
  dpi = 600
)