R update

workflow/envs/R.yaml

@@ -1,16 +1,25 @@
-name: R_env
+name: r_notebook
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - r-base
+  - jupyterlab>3
+  - ipywidgets>=7.6
+  - nbconvert
+  - pandas
+  - r-irkernel
+  - r-tidyverse
   - bioconductor-ggtree
-  - bioconductor-treeio
   - bioconductor-ggtreeextra
-  - r-ggplot2
-  - r-ape
-  - r-dplyr
-  - r-argparser
-  - r-aplot
-  - r-tidytree
+  - r-plotly
+  - r-ggstar
+  - r-repr
+  - r-irdisplay
+  - r-pbdzmq
+  - r-devtools
+  - r-phytools
+  - pandoc
+  - rpy2
+  - jupyter_contrib_nbextensions
+  - r-argparser

workflow/scripts/ggtree.R

@@ -61,9 +61,9 @@ p <- ggtree(tree) %<+% tree_data
 
 
 # DRAW TREE
-g <- p + geom_tiplab(offset = .005, 
-                     hjust = 0.005, 
-                     align=TRUE, 
+g <- p + geom_tiplab(#offset = .005,
+                     #hjust = 0.005,
+                     #align=TRUE,
                      size = 3.2) +
   geom_tippoint(aes(shape = cluster_name, color = cluster_name)) + 
   theme(legend.position = "right") +