graph improvement

bin/donut.R

@@ -538,7 +538,7 @@ if(nrow(obs) > 0){
     }
     if(kind == "annotated" & all.annotation.log == TRUE){ # overwrite final.plot
         # no need to use pdf(NULL) with fun_gg_empty_graph()
-        final.plot <- fun_gg_empty_graph(text = "NO DONUT PLOTTED\nNO ANNOTATION DETECTED", text.size = 3, title = tempo.title, title.size = 4)
+        final.plot <- fun_gg_empty_graph(text = "NO DONUT PLOTTED\nNO SEQUENCE NAME REPLACEMENT DETECTED\n(meta_name_replacement PARAMETER OF THE nextflow.config FILE)", text.size = 3, title = tempo.title, title.size = 4)
     }
 }else{
     final.plot <- fun_gg_empty_graph(text = "NO DONUT PLOTTED\nNO SEQUENCE DETECTED", text.size = 3, title = tempo.title, title.size = 4)

bin/germ_tree_vizu.R

@@ -896,7 +896,7 @@ if(length(tempo.list) == 0){
                     ))
                 }
                 if( ! any(germ_tree_kind %in% c("circular", "fan", "equal_angle", "daylight"))){
-                    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggtree::geom_treescale(width = 0.01, offset = 0.05))
+                    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggtree::geom_treescale(width = 0.01, offset = 0.05, fontsize = 1.5, linesize = 0.25))
                 }
                 assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::theme(plot.margin = ggplot2::margin(t = 0.25, l = 0.1, b = 0.1, r = germ_tree_right_margin, unit = "in")))
                 # legend

nextflow.config

@@ -55,10 +55,10 @@ env {
     germ_tree_kind = "rectangular" // single character string of the kind of tree. Can be "rectangular", "roundrect", "slanted", "ellipse", "circular", "fan", "equal_angle", "daylight". See https://yulab-smu.top/treedata-book/chapter4.html#tree-layouts
     germ_tree_duplicate_seq = "FALSE" // single character string indicating if identical sequences (with difference cell or sequence names) must be removed from trees or not. Either "TRUE" for keeping or "FALSE" for removing
     germ_tree_leaf_color = "NULL" // single character string of the color of leaf tip. Ignored if meta_legend parameter is a name of a non numeric column of the meta_path parameter
-    germ_tree_leaf_shape = "23" // single character string of the shape of leaf tip. See http://127.0.0.1:25059/library/graphics/html/points.html
+    germ_tree_leaf_shape = "21" // single character string of the shape of leaf tip. See https://stat.ethz.ch/R-manual/R-devel/library/graphics/html/points.html
     germ_tree_leaf_size = "3" // single character string of the size of leafs (positive numeric value in mm, the size of the plot being 120 x 120 mm). Ignored if meta_legend parameter is a name of a numeric column of the meta_path parameter
     germ_tree_label_size = "2" // single character string of the size of leaf labeling (positive numeric value in mm, the size of the plot being 120 x 120 mm)
-    germ_tree_label_hjust = "-0.5" // single character string of the adjustment of leaf labeling (numeric value)
+    germ_tree_label_hjust = "-0.2" // single character string of the adjustment of leaf labeling (numeric value)
     germ_tree_label_rigth = "FALSE" // single character string of the position of the labeling. Either "TRUE" or "FALSE". Only works for germ_tree_kind = "rectangular" and users need to use theme() to adjust tip labels in this case
     germ_tree_label_outside = "TRUE" // single character string of the display of the labeling outside of the plot region (if labels are truncated). Either "TRUE" or "FALSE"
     germ_tree_right_margin = "1.5" // single character string of the positive numeric value for the right margin in inches, considering 5 inches the width of the graphic device