jupyter magic commands

Jupyter provides a number of magic commands, allowing you to integrate external functions and methods that are not natively found in RevBayes into your RevBayes workflow.

To list the magic commands available in Jupyter:



In [1]:

    
%lsmagic









    



Available line magics:
%activity  %cd  %connect_info  %conversation  %dot  %download  %edit  %get  %help  %html  %include  %install  %install_magic  %javascript  %jigsaw  %kernel  %kx  %latex  %load  %ls  %lsmagic  %macro  %magic  %matplotlib  %parallel  %plot  %pmap  %px  %python  %reload_magics  %restart  %run  %scheme  %set  %shell

Available cell magics:
%%activity  %%brain  %%conversation  %%debug  %%dot  %%file  %%help  %%html  %%javascript  %%kx  %%latex  %%macro  %%pipe  %%processing  %%px  %%python  %%scheme  %%shell  %%show  %%time  %%tutor

Simulate a tree in `RevBayes`

Suppose we simulate and save a Tree object to file using writeNexus in RevBayes. We can then open that tree file from within the same Juptyer notebook using the %python magic command.

First, create and save the Tree object



In [2]:

    
n_taxa = 10
for (i in 1:n_taxa) {
    taxa[i] = taxon("T"+i, 0.0)
}
phy ~ dnBDP(lambda=1, rootAge=1, taxa=taxa)
writeNexus(data=phy, filename="example/output/magic_test.tre")

Open output in `tracer`

Let's view the tree in FigTree. Launch terminal commands using the magic function %shell



In [3]:

    
%shell figtree example/output/magic_test.tre

Of course, this example relies on figtree existing in the user's environment PATH variable.

Executing `python` code

Use %%python to indicate the next cell conatins python commands



In [4]:

    
%%python

# python packages
import dendropy
from Bio import Phylo

# the tree's filename
phy_fn = 'example/output/magic_test.tre'

# visualize a tree in Dendropy
dtree = dendropy.Tree.get(path=phy_fn,schema='nexus')
print('Dendropy\n'+dtree.as_ascii_plot())

# visualize a tree in Biopython
bptree = Phylo.read(phy_fn, 'nexus')
Phylo.draw(bptree)









    



Dendropy
                                                                                               /----------------------- T1 
                                                                       /-----------------------+                           
                                                                       |                       \----------------------- T10
                                               /-----------------------+                                                   
                                               |                       |                       /----------------------- T3 
/----------------------------------------------+                       \-----------------------+                           
|                                              |                                               \----------------------- T9 
|                                              |                                                                           
|                                              \----------------------------------------------------------------------- T6 
|                                                                                                                          
+                                              /----------------------------------------------------------------------- T5 
|                                              |                                                                           
|                      /-----------------------+                                               /----------------------- T8 
|                      |                       |                       /-----------------------+                           
|                      |                       \-----------------------+                       \----------------------- T7 
\----------------------+                                               |                                                   
                       |                                               \----------------------------------------------- T4 
                       |                                                                                                   
                       \----------------------------------------------------------------------------------------------- T2

This draws the tree in a pyplot window. Full-featured kernels enable inline figure presentation through the magic command "%matplotlib inline". Unfortunately, this is not currently supported in metakernel (link). I've made no progress so far on a workaround.

Executing `R` code through `rpy2`

R does not natively support magic commands. However, we can the package rpy2 to execute R commands through the %%python environment.



In [5]:

    
%%python

# python packages
from rpy2.robjects import r
import dendropy

# read tree into dendropy
phy_fn = 'example/output/magic_test.tre'
dtree = dendropy.Tree.get(path=phy_fn,schema='nexus')

# extract Newick string from file
phy_str = dtree.as_string("newick")

# parse Newick string in R
rtree = r("""
library('ape')
phy_r=read.tree(text='%s')
""" % phy_str)

# read the R object from the global rpy2 environment
rtree=r['phy_r']
print("ape tree as rpy2 object:")
print(rtree)

# store R values into python
tip_labels = rtree[ rtree.names.index('tip.label') ]
print("Tip labels as rpy2 object:")
print(tip_labels)









    



ape tree as rpy2 object:

Phylogenetic tree with 10 tips and 9 internal nodes.

Tip labels:
	T1, T10, T3, T9, T6, T5, ...

Rooted; includes branch lengths.

Tip labels as rpy2 object:
 [1] "T1"  "T10" "T3"  "T9"  "T6"  "T5"  "T8"  "T7"  "T4"  "T2"

Importing `python` objects into `RevBayes`

This feature is slated for future development.

jupyter magic commands

Simulate a tree in RevBayes

Open output in tracer

Executing python code

Executing R code through rpy2

Importing python objects into RevBayes

Simulate a tree in `RevBayes`

Open output in `tracer`

Executing `python` code

Executing `R` code through `rpy2`

Importing `python` objects into `RevBayes`