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Showing content from https://github.com/grunwaldlab/metacoder/issues/197 below:

heat_tree_matrix expects pairs of treatments to be in a specific order · Issue #197 · grunwaldlab/metacoder · GitHub

It expects treatments to be paired like so:

Browse[2]> treatments
[1] "rhizogenes"  "tumefaciens" "vitis"      
Browse[2]> combinations
     [,1] [,2]
[1,]    1    2
[2,]    1    3
[3,]    2    3

but an arrangement like this would also be valid:

     [,1] [,2]
[1,]    1    2
[2,]    3    1
[3,]    2    3

or

     [,1] [,2]
[1,]    1    2
[2,]    3    1
[3,]    3    2

This is fine if the data was produced with compare_groups, but a nuisance if the data set came from somewhere else.

This results in some subplots not getting data


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