Summary PDFs

Summary PDFs#

Before playing around with the KSTAR results, you may first wish to get an initial idea of the results from KSTAR. We have provided the ability to quickly a summary PDF file that quickly compiles and summarizes the parameters used, a quick plot of the results, and the underlying evidence characteristics. This notebook shows you how to create this PDF

Note: if you set create_summary_pdf=True in the ``run_kstar_analysis`` function, this will automatically be created in the RESULTS folder

Creating the PDF#

The easiest way to do this is directly from the KinaseActivity object, which can be accomplished either if activities have just been calculated or if you saved your KSTAR results with the save_kstar() function.

First, if needed, load the KinaseActivity object.

[2]:

from kstar import calculate

odir = './example'
name = 'example_run'
kinact_dict = calculate.from_kstar(odir = odir, name = name)

Next, we just need to run the KinaseActivity function called make_summary_pdf(), using either ‘Y’ or ‘ST’ results.

[3]:

kinact_dict['Y'].make_summary_pdf()

generating dotplot figure...

Resulting PDF Files#

The PDF will be saved within the indicated output directory. It will consist of three pages:

  1. Summary Page: indicates key parameters used and the top kinases identified within each sample

  2. DotPlot Page: a basic DotPlot showing only significant kinases

  3. Evidence Page: summarizes number of sites used as evidence for each sample and the similarity between them

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