Merge pull request nf-core#47 from Eco-Flow/Better_tree_plots

new plots organisation
stephenturner · Oct 24, 2024 · 63065f3 · 63065f3
2 parents b6f060e + 0cf0dd0
commit 63065f3
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/bin/plot_tree_summary.R b/bin/plot_tree_summary.R
@@ -129,16 +129,18 @@ for (i in 2:length(column_headers)) {
   if (plot_type == "bar") {
     bar_plot <- ggplot(data, aes(x = as.numeric(!!sym(column_name)), y = factor(species, levels = rev(tree$tip.label)))) + 
       geom_bar(stat = "identity", fill = "darkblue") + 
-      geom_text(aes(label = !!sym(column_name)), hjust = -0.1, size = args$text_size) +  # Add text labels
+      geom_text(aes(label = as.numeric(!!sym(column_name)), x = 0), hjust = -0.1, color = "white", size = args$text_size) +  # Place text at the base of the bar
       theme_minimal() + 
       theme(axis.title.y = element_blank(), 
             axis.text.y = element_blank(),
             axis.ticks.y = element_blank(),
             axis.title.x = element_blank(), 
             axis.text.x = element_blank(),
             axis.ticks.x = element_blank(),
-            panel.grid.major.y = element_blank(),  # Remove horizontal grid lines
-            panel.grid.minor.y = element_blank(),
+            panel.grid.major = element_blank(),  # Remove vertical grid lines
+            panel.grid.minor = element_blank(),  # Remove minor grid lines
+            panel.background = element_blank(),  # Remove grey background
+            plot.background = element_blank(),   # Remove any outer plot background
             plot.margin = margin(0, 0, 0, 0)) + 
       labs(x = column_name) +
       ggtitle(column_name)

diff --git a/bin/plot_tree_summary2.R b/bin/plot_tree_summary2.R
@@ -88,7 +88,7 @@ tree_plot <- ggtree(tree) +
   geom_tiplab() + 
   coord_cartesian(clip="off") +
   ggtitle("Phylogenetic Tree") +
-  theme(plot.margin = margin(10, 150, 10, 10))  # Increase margins
+  theme(plot.margin = margin(10, 70, 10, 10))  # Increase margins
 
 pdf ("Tree_only.pdf")
 tree_plot

diff --git a/modules/local/tree_summary.nf b/modules/local/tree_summary.nf
@@ -37,8 +37,8 @@ process TREE_SUMMARY {
     sed \'s/.prot.fa.largestIsoform.fa//g\' Quast_to_plot.tsv > Quast_to_plot_final.tsv
 
     # Run summary plot
-    /usr/bin/Rscript ${projectDir}/bin/plot_tree_summary2.R tree.nw Busco_to_plot_final.tsv
-    /usr/bin/Rscript ${projectDir}/bin/plot_tree_summary.R  tree.nw Quast_to_plot_final.tsv
+    /usr/bin/Rscript ${projectDir}/bin/plot_tree_summary2.R tree.nw Busco_to_plot_final.tsv --tree_size 0.6
+    /usr/bin/Rscript ${projectDir}/bin/plot_tree_summary.R  tree.nw Quast_to_plot_final.tsv --tree_size 0.6
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":