bokeh org-mode

Introduction

This is an illustration of how to use bokeh with org-mode in nikola. There is a more extensive and flexible explanation of how to do this in this post on cherian.net but I made these notes to understand how it works and to have a simpler example to refer to.

I was interested in doing this because I'm trying to re-work some of what I did for the Coursera Data Science With Python specialization by changing the data-sets and building them as blog posts. I might convert the posts to restructured text at some point, but while I'm working with them I'm using org-mode. Also, while most of the time I use matplotlib for plotting since this is going to be a blog-first approach I decided to go with bokeh. I had previously written about how to gut bokeh into Nikola using restructured text, but as an intermediate step I want to do the work in org-mode and still be able to see the output as I'm working.

The magic mix for this seems to be to use:

Creating the Bokeh Plot

Imports

These are the dependencies. It's really all bokeh, numpy is just there to generate the data-values.

# from pypi
from bokeh.models import HoverTool
from bokeh.plotting import figure, ColumnDataSource
from bokeh.embed import autoload_static, file_html
import bokeh.resources
import numpy

I probably should save bokeh to this repository to keep the post from breaking in the future, but I'm lazy so I'm just going to import it from a CDN.

bokeh = bokeh.resources.CDN

The Data

To get a simple example going I'm just going to use some random outputs generated by numpy.

X = numpy.arange(10)
Y = numpy.random.randint(0, 10, 10)

In order to create a data-structure that bokeh can use (similar to a pandas dataframe) you need to use a ColumnDataSource.

source = ColumnDataSource(data=dict(
    x=X,
    y=Y,
    desc=["a", "b", "c", "d", "e", "f", "g", "h", "i", "j"],
))

The keys in the data-dict are essentially the column headers.

Key Description
x the x-axis values
y the y-axis values
desc The labels for the tooltip

Now to get some tool-tips to pop up when you hover over the plot, I'll create a HoverTool.

hover = HoverTool(tooltips=[
    ('index', '$index'),
    ('(x, y)', '($x, $y)'),
    ('desc', '@desc'),
])

The tooltips list maps the labels that will show up in the tooltip (the first argument to each tuple) to variables in the ColumnDataSource (if preceded by an @) or generated value (if preceded by a $) The index value is the index in the array where the data point sits (so for the first point it will be 0, the second will be 1, etc.). The (x, y) values are the coordinate locations of your pointer when you hover over the data points, and the desc will be replaced by the label I set in the ColumnDataSource for a particular data-point.

The Plot

Now I'll create the actual plot (figure).

fig = figure(title="Random Example", x_axis_label="x", y_axis_label="y",
	     tools=[hover])
fig.line('x', 'y', source=source)
fig.circle('x', 'y', size=10, source=source)

Getting the Bokeh Plot Into The Post

Finally I'll save the javascript and HTML files needed and then output the blob needed to embed the plot into this post. The autoload_static function takes the bokeh plot object (fig), the bokeh javascript that I loaded earlier (bokeh), and the name of the javascript file that you want it to creat (test.js) and returns the javascript to save (javascript) and the HTML fragment that will include the javascript (source). Note that because of the way nikola structures things I have to create a folder named files/posts/bokeh-org-mode and save the files there. Since nikola will automatically look in this folder the name you pass into autoload_static should just be the filename without the path, but when you save the javascript file you will save it there so you need to add the relative path. If my explanation seems a little convoluted, just look at the code below, it's fairly simple.

First I'll create a variable to hold the path to the folder to save the files in. All files for nikola posts go into sub-folders of files/posts/ and since the source file for this post is called bokeh-org-mode.org, the files to include in it go into the folder files/posts/bokeh-org-mode (files/posts/ plus the slug for the post).

FOLDER_PATH = "../files/posts/bokeh-org-mode/"

The Javascript

Now, I'll create the javascript source for the plot.

FILE_NAME = "test.js"
javascript, source = autoload_static(fig, bokeh, FILE_NAME)

with open(FOLDER_PATH + FILE_NAME, "w") as writer:
    writer.write(javascript)

The javascript variable holds the actual javascript source code (which then gets saved) while the source variable holds the string with the HTML to embed the javascript into this post (which I show at the end of this post).

Embedding the Plot

Finally, we need to print out the string that is stored in the source variable which then tells org-mode to embed the files into this post. I'll output the full org-block so you can see the header arguments.

#+BEGIN_SRC python :session bokeh :results output raw :exports results
print('''#+BEGIN_EXPORT html
{}
#+END_EXPORT'''.format(source))
#+END_SRC

And there you have it. I don't have a lot to say about it, other than that if you hover over the data with your cursor and then look up above at the ColumnDataSource above, you'll see that the variables match the inputs

Summary

To get a bokeh figure into an org-mode document in nikola:

  1. Create the bokeh plot.
  2. Create a folder in the files/posts/ folder that matches the slug for the post.
  3. Use autoload_static to convert the bokeh object to javascript and create the HTML tag to embed it.
  4. Save the javascript in the files/posts/<slug>/ folder that you created
  5. Print the HTML fragment in an org-mode #+BEGIN_EXPORT html block.