Tutorial

To run MAGIC on your dataset, create a MAGIC operator and run fit_transform. Here we show an example with an artificial test dataset located in the MAGIC repository:

import magic
import matplotlib.pyplot as plt
import pandas as pd
X = pd.read_csv("MAGIC/data/test_data.csv")
magic_operator = magic.MAGIC()
X_magic = magic_operator.fit_transform(X, genes=['VIM', 'CDH1', 'ZEB1'])
plt.scatter(X_magic['VIM'], X_magic['CDH1'], c=X_magic['ZEB1'], s=1, cmap='inferno')
plt.show()
magic.plot.animate_magic(X, gene_x='VIM', gene_y='CDH1', gene_color='ZEB1', operator=magic_operator)

A demo on MAGIC usage for single cell RNA-seq data can be found in this notebook: http://nbviewer.jupyter.org/github/KrishnaswamyLab/magic/blob/master/python/tutorial_notebooks/emt_tutorial.ipynb

A second tutorial analyzing myeloid and erythroid cells in mouse bone marrow is available here: http://nbviewer.jupyter.org/github/KrishnaswamyLab/magic/blob/master/python/tutorial_notebooks/bonemarrow_tutorial.ipynb