Get started
Install DREEM (if not already done)
Note
You don’t need any non-pythonic dependency to use DREEM for plotting only. If you want to process your data with DREEM, you will need to install the Dependencies.
Install DREEM with pip. Use Python = 3.10 ONLY
pip install dreem
Note
We recommend that you create a virtual environment with Python 3.10 to avoid any conflict with other packages.
Example with virtualenv:
python3.10 -m venv dreem_env
source dreem_env/bin/activate
pip install dreem
Example with conda:
conda create -n dreem_env python=3.10
conda activate dreem_env
pip install dreem
Import your data into a study object
from dreem.draw import study
import json
# Define the list of samples you want to load
my_samples = ['my_sample_1', 'my_sample_2', 'my_sample_3']
# Load the data as a list of dictionaries
data = []
for sample in my_samples:
with open('{}.json'.format(sample), 'r') as f:
data.append(json.load(f))
# Create a study object
my_study = study.Study(data)
# Print the list of available samples
print(my_study.get_samples())
Make a plot
study.mutation_fraction(
sample='my_sample_1',
reference = 'my_reference_1',
section = 'my_section_1',
cluster = 'pop_avg'
)
Note
We regularly update the list of available plots. Make sure that you have the last version of DREEM.