minor fixes in the appearance of the plots

src/plotting/ExtendedDataFigure2.R

@@ -114,7 +114,7 @@ f_helper_plot_diversity <- function(c_comparison, c_name) {
     # Just use the ggsignif function for plotting the p-value symbols
     ggsignif::geom_signif(
       comparisons = c_comparison_list,
-      #annotations = p_to_symbol(p_adj_vec_shannon),
+      annotations = p_to_symbol(p_adj_vec_shannon),
       vjust = -0, step_increase = 0.075, textsize = 3
     )
 
@@ -136,6 +136,7 @@ f_helper_plot_diversity <- function(c_comparison, c_name) {
 
   return(list(richness = pt_richness, shannon = pt_shannon, pcoa = pt_pcoa))
 }
+
 i <- 1
 comparison_list
 figure_indices <- c("A","B","C","E","F","G","I","J","K")
@@ -145,7 +146,7 @@ h <- 4.5
 for(i in seq(1,length(comparison_list))){
   # loop through the comparisons and generate the plots
   res <- f_helper_plot_diversity(c_comparison = comparison_list[[i]], c_name = comparison_name[i])
-  
+
   # save the plots
   ggsave(paste0(save_fig_folder,"/",figure_indices[id],"_SpeciesRichness.pdf"), res$richness, width = w, height = h)
   id <- id + 1
@@ -178,7 +179,7 @@ pt_D <- f_plot_volcano(
   plot_df = plot_df, xBreaks = xBreaks, xLims = xLims,
   man_y_breaks = man_y_breaks
 ) +
-  scale_fill_manual(values = group_colors)+
+  scale_fill_manual(values = group_colors, drop = F)+
   size_definition
 
 # CRLM vs non-TUmor CRLM
@@ -190,7 +191,7 @@ pt_H <- f_plot_volcano(
   plot_df = plot_df, xBreaks = xBreaks, xLims = xLims,
   man_y_breaks = man_y_breaks
 ) +
-  scale_fill_manual(values = group_colors)+
+  scale_fill_manual(values = group_colors, drop = F)+
   size_definition
 
 
@@ -207,7 +208,7 @@ pt_L <- f_plot_volcano(
   plot_df = plot_df, xBreaks = xBreaks, xLims = xLims,
   man_y_breaks = man_y_breaks
 ) +
-  scale_fill_manual(values = group_colors)+
+  scale_fill_manual(values = group_colors, drop = F)+
   size_definition
 
 # iCCA vs GBC #! Note: Labels are swapped compard to the manuscript figure (iCCA is on the left in the manuscript). Values are all the same with swapped sign.
@@ -219,7 +220,7 @@ pt_M <- f_plot_volcano(
   plot_df = plot_df, xBreaks = xBreaks, xLims = xLims,
   man_y_breaks = man_y_breaks
 ) +
-  scale_fill_manual(values = group_colors)+
+  scale_fill_manual(values = group_colors, drop = F)+
   size_definition
 
 # GBC vs phCCA/dCCA #! Note: Labels are swapped compard to the manuscript figure (iCCA is on the left in the manuscript). Values are all the same with swapped sign.
@@ -230,7 +231,7 @@ xLims <- c(-0.51,1.1)
 pt_N <- f_plot_volcano(
   plot_df = plot_df, xBreaks = xBreaks, xLims = xLims,
   man_y_breaks = man_y_breaks) +
-  scale_fill_manual(values = group_colors)+
+  scale_fill_manual(values = group_colors, drop = F)+
   size_definition
 
 

src/plotting/ExtendedDataFigure4.R

@@ -275,7 +275,7 @@ pt_box_RNAseq <-
 
 # Combine the two boxplots
 pt_box_combined <- (pt_box_16S+theme(axis.text.x = element_blank(),axis.ticks.x = element_blank())) / pt_box_RNAseq
-ggsave(pt_box_combined ,filename = file.path(save_fig_folder,"C_Boxplot_5R16SvsBulkRNAseq_DKFZ.pdf"), width = 5, height = 5)
+ggsave(pt_box_combined ,filename = file.path(save_fig_folder,"C_Boxplot_5R16SvsBulkRNAseq_DKFZ.pdf"), width = 12, height = 8)
 
 
 #* Panel D: Pairsplot of genus level relative abundances for all datasets against each other ----

src/plotting/ExtendedDataFigure6.R

@@ -273,7 +273,7 @@ plot_df <- all_test_results_df %>% filter(comparison == "Fibrosis_late_vs_HCC")
 plot_df$Group1 <- str_replace(plot_df$Group1,"LateFib","Fibrosis late stage")
 plot_df$Group2 <- str_replace(plot_df$Group2,"LateFib","Fibrosis late stage")
 range(plot_df$effect.size)
-xBreaks <- round(seq(-0.8,0.3,0.1),1)
+xBreaks <- round(seq(-0.8,0.4,0.2),1)
 xLims <- range(xBreaks)
 pt_E <- f_plot_volcano(
   plot_df = plot_df, xBreaks = xBreaks, xLims = xLims,

src/plotting/Figure2.R

@@ -108,7 +108,7 @@ pt_B <- meanAB_df %>%
   geom_abline(slope = 1, intercept = 0) +
   tune::coord_obs_pred() +
   theme_paper +
-  scale_fill_manual(values = phylum_colors_vec)+
+  scale_fill_manual(values = phylum_colors_df %>% dplyr::select(phylum,HEX) %>% deframe())+
   annotate("text",
     x = -5, y = 0, hjust = 0, vjust = 0.75, size = 3,
     # annotate("text", x = -2, y = -3.7, hjust = 0, vjust = 0.75,size = 3,

src/plotting/Figure3.R

@@ -167,7 +167,7 @@ pt_B <- plot_df %>%
   scale_fill_manual(values = col_vec, labels = col_labs) +
   geom_hline(yintercept = -log10(0.05)) +
   # label highly significant genes of other pathways
-  ggrepel::geom_text_repel(data = plot_df %>% filter(pathway_association == "other", -log10(p.val_adj) > 8 | (effect.size > 0 & -log10(p.val_adj) > 6) | effect.size > 0.4), aes(label = gene), color = "darkgrey", size = 3)+
+  ggrepel::geom_text_repel(data = plot_df %>% filter(pathway_association == "other", -log10(p.val_adj) > 8 | (effect.size > 0 & -log10(p.val_adj) > 6) | effect.size > 0.4), aes(label = gene), color = "darkgrey", size = 3) +
 
   # label highly significant genes of inflammatory pathways and metabolic pathways
   ggrepel::geom_label_repel(data = plot_df %>% filter(pathway_association != "other", -log10(p.val_adj) > 2), aes(label = gene, fill = pathway_association), color = "black", alpha = 0.85, show.legend = F, size = 3) +
@@ -177,7 +177,13 @@ pt_B <- plot_df %>%
   ggtitle("Gene expression differnces depending on total bacterial load") +
   labs(fill = "") +
   ylab("-log10 q-value") +
-  xlab("Enrichment effect size")
+  xlab("Enrichment effect size") +
+  theme(
+    legend.title = element_blank(),
+    legend.position = c(1, 1),
+    legend.justification = c(1, 1),
+    legend.margin = margin(6, 6, 6, 6)
+  )
 
 ggsave(pt_B, filename = file.path(save_fig_folder, "B_Volcano_TotalBacteriaVSgeneExpression.pdf"), width = 7, height = 8)