add node labes like n# if no taxa matches a given MRCA

waldronlab · Sep 11, 2023 · e803ea5 · e803ea5
1 parent 9a20c1b
commit e803ea5
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Showing 3 changed files with 5 additions and 11 deletions.
diff --git a/inst/extdata/livingTree.newick b/inst/extdata/livingTree.newick
diff --git a/inst/scripts/get_living.tree.R b/inst/scripts/get_living.tree.R
@@ -26,7 +26,6 @@ not_missing_anymore_taxa <- taxizedb::name2taxid(missing_taxa, db = 'ncbi')
 taxids[which(is.na(taxids))] <- not_missing_anymore_taxa
 
 taxonomy <- taxizedb::classification(unique(taxids), db = 'ncbi')
-x <- taxonomy
 missing_taxonomy_positions <- which(map_lgl(taxonomy, ~ all(is.na(.x))))
 not_missing_anymore_taxonomy <- taxize::classification(
     names(missing_taxonomy_positions), db =  'ncbi'
@@ -99,8 +98,8 @@ mrcas_df <- mrcas_df |>
 nodes <- data.frame(node = length(tree$tip.label) + 1:tree$Nnode) |>
     left_join(mrcas_df, by = 'node') |>
     mutate(
-        node_label = ifelse(is.na(node_label), '', node_label),
-        n_labels = ifelse(is.na(n_labels), 0, n_labels)
+        node_label = ifelse(is.na(node_label), paste0('n', node), node_label),
+        n_labels = ifelse(is.na(n_labels), 0, n_labels),
     )
 
 tree$node.label <- nodes$node_label

diff --git a/vignettes/articles/phytools.Rmd b/vignettes/articles/phytools.Rmd
@@ -139,12 +139,8 @@ phys_data_ready <- left_join(set_with_ids, set_without_ids)
 
 
 
-```{r}
-tree <- ltp()
-system.time(
-    data_tree <- as.Node(tree, heightName = NULL)
-)
-```
+
+
 
 
 
@@ -275,4 +271,3 @@ plot(ace, args.plotTree = list(direction = "upwards"))
 tips <- sapply(labs, function(x, y) which(y == x), y = tree$tip.label)
 add.arrow(tree, tips, arrl = 3, offset = 2, lwd = 2, col = palette()[4])
 ```
-