Pandora Python Library Examples

In addition to the command line, all of Pandora’s functionality can be used as Python library with an additional interface for any kind of numpy data matrix. The idea is that many (computational) biologists use R or Python to perform their PCA and MDS analyses instead of using smartpca. This enables the user to perform any kind of preprocessing before doing the PCA/MDS analyses.

In the following, I will provide examples on how to use the numpy-based interface for PCA and MDS analyses. Since Pandora of course also has the Eigenfiles-based interface available in the Python library, I will also demonstrate how to use this interface.

Examples

• NumPy-based interface
  • PCA Analysis
  • MDS Analysis
    • Custom distance metric
  • Sliding-Window Analysis
  • Loading Eigen-files as NumpyDataset
• EIGEN-based interface
• Plotting and further insights
• Working with R exports