fix: changed the figure 1 and 3

scripts/metadata.R

@@ -27,12 +27,16 @@ ann$rin <- scale(ann$rin)[,1]
 rownames(ann) <- ann$sample_id
 ann$sample_id <- NULL
 
+# Keep the full dataframe
+ann_full <- ann
+
 # Remove samples "SRR5961961" and "SRR5961809" that appeared as outliers on robust pca analysis
 ann <- ann %>%
   filter(!(rownames(ann) %in% c("SRR5961961", "SRR5961809")))
 
 # Save (this metadata will be used in all future models)
 save(ann, file = "results/important_variables/ann.rda")
+save(ann_full, file = "results/important_variables/ann_full.rda")
 
 
 

scripts/network.R

@@ -82,9 +82,6 @@ addGraph(rdp, g)
 nodes <- read_tsv("results/networks/model_nodes.txt")
 edges <- read_delim("results/networks/model_edges.txt")
 
-nodes <- read_tsv("~/model_nodes.txt")
-edges <- read_delim("~/model_edges.txt")
-
 # Import nodes coordinates determined by vivagraph
 layout <- read.csv("results/networks/layout.csv")
 
@@ -109,16 +106,16 @@ ggraph(g, x = x, y = y) +
     data = as_data_frame(g, "vertices") %>% filter(gwas == "gwas"),
     colour = NA,
     n = 5,
-    pie_scale = 0.5,
+    pie_scale = 0.9,
   show.legend = F) +
   geom_scatterpie(
     cols = c("a", "b", "c"),
     data = as_data_frame(g, "vertices") %>% filter(gwas == "not_gwas"),
     colour = NA,
-    pie_scale = 0.2,
+    pie_scale = 0.3,
     show.legend = F
   ) +
-  geom_node_text(aes(label = alias), size = 0.9, nudge_x = 2, nudge_y = 4) + 
+  #geom_node_text(aes(label = alias), size = 1.7, nudge_x = 2, nudge_y = 4) + 
   #geom_node_label(aes(label = alias)) + 
   scale_fill_manual(values = c("#0ac80aff", "#4f4affff", "#ff822fff")) +
   coord_fixed() +
@@ -130,7 +127,7 @@ if(!dir.exists("results/plots_paper/")) {
   dir.create("results/plots_paper")
 }
 
-svg(filename = "results/plots_paper/network.svg", height = 10, width = 10)
+pdf(file = "~/Área de Trabalho/network.pdf", height = 15, width = 15)
 print(p)
 dev.off()
 

scripts/plots.rmd

@@ -355,9 +355,45 @@ ggsave("results/plots_paper/fig2C_2.png", height = 4, width = 5, dpi = 300)
 
 ```
 
-## Figure 3
+# Figure 3
 
-Figure 3 was produced on the biotype analysis, in the `summarise_biotypes.R` script.
+```{r}
+# Load enrichment data
+load("results/tx_enrich/go_terms_tx_by_group.rda")
+
+# Create a dataframe with results from OFC (female) and CG25 (male) enrichment
+df_enrich <- bind_rows(enriched_df_diff[["OFC_female"]], enriched_df_diff[["Cg25_male"]])
+
+# Parse gene ratio column
+df_enrich <- df_enrich %>%  mutate(
+  n_tag = as.numeric(sapply(strsplit(GeneRatio, split = "\\/"), "[[", 2)),
+  GeneRatio = as.numeric(Count) / n_tag
+)
+
+# Plot
+df_enrich %>% 
+  ggplot(aes(x = fct_reorder2(Description, -p.adjust, -Count), y = GeneRatio, size = Count, col = p.adjust)) +
+  geom_point() +
+  facet_grid(rows = vars(group), scales = "free_y", space = "free_y",
+             labeller = as_labeller(c(
+               "Cg25_male" = "Cg25 (male)",
+               "OFC_female" = "OFC (female)"
+             ))) +
+  force_panelsizes(rows = c(0.17, 1)) +
+  scale_color_continuous(limits = c(0, 0.05), breaks = seq(0, 0.05, 0.01)) +
+  labs(x = "", y = "Gene ratio", color = "FDR", size = "Intersection") +
+  coord_flip() + 
+  theme_bw() +
+  theme(axis.text.y = element_text(size = 9),
+        strip.text.y = element_text(size = 9))
+
+ggsave(filename = "results/plots_paper/fig3.pdf", width = 9, height = 6)
+ggsave(filename = "results/plots_paper/fig3.png", width = 9, height = 6)
+```
+
+## Figure 4
+
+Figure 4 was produced on the biotype analysis, in the `summarise_biotypes.R` script.
 
 
 # Supplementary Figures