20251008 Analysis
!pip install nucleus-cdk==0.5.0rc2 | tail -n2
# Surface a failed install here, rather than as a confusing ModuleNotFoundError
# in the import cell below.
import importlib.metadata as md
assert md.version("nucleus-cdk") == "0.5.0rc2", f"got {md.version('nucleus-cdk')}"
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from cdk.analysis.cytosol import platereader as pr
import warnings
warnings.filterwarnings('ignore')
# Initialize plotting
pr.plot_setup()Requirement already satisfied: asttokens in /opt/homebrew/anaconda3/lib/python3.12/site-packages (from stack-data->ipython>=6.1.0->ipywidgets==8.*->jupyter-bokeh<5.0.0,>=4.0.5->nucleus-cdk==0.5.0rc2) (2.0.5)
Requirement already satisfied: pure-eval in /opt/homebrew/anaconda3/lib/python3.12/site-packages (from stack-data->ipython>=6.1.0->ipywidgets==8.*->jupyter-bokeh<5.0.0,>=4.0.5->nucleus-cdk==0.5.0rc2) (0.2.2)
Load the data¶
Provide a CSV file containing the data, and a platemap. This function returns both the data with the plate map mapped to it, and the platemap by itself, which is useful for certain tasks.
data_file = "./20251008-125648-cytation5-pure-timecourse-gfp--biotek-cdk.txt"
platemap_file = "20251008-ClpXP-new.csv"
data, platemap = pr.load_platereader_data(data_file, platemap_file)Basic Analysis¶
Curves¶
Curves of RFU over time, by named sample.
pr.plot_curves(data);