The Kitchin Research Group

I have found using tables in an org-file as data sources to code blocks very convenient for documenting work. A typical work flow might go like this:

1. Use a code block to generate some data in an org-table.
2. Use another code block to analyze the data.

For example, here is a code block that prints data in a table ¹:

import numpy as np

print '#+tblname: cos-data'
print '| x | cos(x)|'
print '|-'

for x in np.linspace(0, 2*np.pi, 10):
    print '|{0}|{1}|'.format(x, np.cos(x))

Now, we use that table in a code block to plot the data. We do this by using some header arguments to the code block:

#+BEGIN_SRC python :var data=cos-data

Then we can use the data variable inside the code block like this:

import numpy as np
import matplotlib.pyplot as plt

data = np.array(data) # data is a list coming in
x = data[:, 0]
y = data[:, 1]
plt.plot(x, y)
plt.xlabel('x')
plt.ylabel('cos(x)')
plt.savefig('images/cos-plot.png')

That is pretty awesome, but what if we have data in a table from another org-file? It turns out we can use it too. I have data for the sin(x) stored in a table called sin-data in sin.org , which I now want to use. We can access that table like this in a header arg:

#+BEGIN_SRC python :var data=sin.org:sin-data

And now use the data variable just like before!

import numpy as np
import matplotlib.pyplot as plt

data = np.array(data) # data is a list coming in
x = data[:, 0]
y = data[:, 1]
plt.plot(x, y)
plt.xlabel('x')
plt.ylabel('sin(x)')
plt.savefig('images/sin-plot.png')

This is a powerful capability, as it allows you to pull data from other files into your current analysis. For example, the supporting information files from some of our recent publications have org-files embedded in them with data stored in org-tables. You could use that data in your own analysis without having to type it in yourself. The only thing you need to do is make sure each table in a document is uniquely named.

Special thanks to Eric Schulte for pointing out the syntax for using external tables!

Copyright (C) 2014 by John Kitchin. See the License for information about copying.

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