plot_tree, label.tips = "taxa_names" doesn't display if a sample = 0

[jeffkimbrel]

When running plot_tree and displaying taxa (OTU) names, if an OTU has a zero value, the OTU name doesn't display.

See example with 9 samples:

Only those with 9 circles have the taxa_names.

I'm not certain if those are exactly zero values, or just very low. Since the Abundance scale as a small circle when the count=1, I assume those without circles are zeroes.

> R.version
               _                           
platform       x86_64-apple-darwin13.4.0   
arch           x86_64                      
os             darwin13.4.0                
system         x86_64, darwin13.4.0        
status                                     
major          3                           
minor          2.0                         
year           2015                        
month          04                          
day            16                          
svn rev        68180                       
language       R                           
version.string R version 3.2.0 (2015-04-16)
nickname       Full of Ingredients   

> packageVersion("phyloseq")
[1] ‘1.13.2’

> packageVersion("ggplot2")
[1] ‘1.0.1’

Jeff

[jeffkimbrel]

Just to clarify, it looks as though it is only if the first sample on the left is zero, not if any of the samples are zero.

Thanks,

Jeff

[joey711]

Thanks for the careful problem description, Jeff. My first impression is that this is indeed a minor bug. I can't think of the explanation off the top of my head, but I'll tag this for a fix and keep this open until it is solved.

Thanks!

joey

[franccalabrese]

Hi Joey,
about the name list not correctly shown in the "justified" image, I acted directly on the 0 values in the .biom matrix.
I simply replace the 0 otu values with 1. Even though the little spots will correspond to 1, it is easy to discriminate between them and the bigger values.
What do you think about?
Thanks!

Francesco

[franccalabrese]

I tryed to add a mock sample as the first in the biom file, but the problem is the sorting the package does.

Francesco