dotTree with missing data

[HedvigS]

dear Dr @liamrevell

I like phytools::dotTree(), it's simple and handy!

I have a case where I'm plotting discrete values and there are some missing values. I'd like these to be handled differently, but now they're filled in with white which looks like it's part of the scale.

Here's an example:

What I've done here after pruning the tree (poly_tree) and data frame (poly_tree_tip_value_df) with data is this:

colours <- c("#ffffbf","#8856a7")
feature_vec <- poly_tree_tip_value_df$GB409 %>% as.character()

fmode<-as.factor(setNames(poly_tree_tip_value_df$GB409,poly_tree_tip_value_df$Name))


dotTree(ladderize(poly_tree,right = F),x = fmode,colors=setNames(colours,
                                       c("0","1")),fsize=1, legend = F)

I saw your blog post about setting pts to F, but this made no difference I'm afraid.

I see these solutions:

• somehow setting the black circle outline to white or cex 0 for the values that are missing
• getting the phylo.heatmap option to work with the slash
• re-evaluating the missing values to a non-missing values like "?" and map that to a color like grey

What do you think?

Happy for any advice :)

[HedvigS]

I ended up solving this by setting border to "transparent" and those values to white

Not sure if I should leave this issue up in case it ends up going in some documentation somewhere that this is one solution.