Analysis: 20251104
!pip install nucleus-cdk==0.5.0rc2 | tail -n2Requirement 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)
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from cdk.analysis.cytosol import platereader as pr
# Initialize plotting
pr.plot_setup()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 = "./20251104-cytation3-pure-timecourse-gfp-NucleusPURE_deGFP-biotek-cdk.txt"
platemap_file = "./20251104-NucleusPURE-deGFP-platemap.csv"
data, platemap = pr.load_platereader_data(data_file, platemap_file)Basic Analysis¶
Curves¶
Curves of RFU over time, by named sample.
K=pr.plot_curves(data)
K.savefig('Kinetics')
K2=pr.plot_curves(data, units="Well", estimator=None)
K2.axes.flatten()[0].axvline(pd.to_timedelta("04:00:00"), c="red", ls="--")
K2.savefig('Kinetics2')
Steady state¶
Bar graph of steady-state endpoint of each sample. Steady state is calculated as the maximum fluorescence value over a 3-sample rolling average on the data.
g = sns.catplot(
data=data[data["Time"] == "04:00:00"],
x="Name",
y="Data",
kind="bar"
)
g.set_xticklabels(rotation=90)
g.savefig('Steadystate')
S= pr.plot_steadystate(data)
S.savefig('endpoint')
Kinetics¶
These functions calculate key kinetic parameters of the time series.
pr.plot_kinetics(data)PROVIDING AVERAGED KINETICS
(<seaborn.axisgrid.FacetGrid at 0x30c13e850>,
Velocity \
Time
Name Read
Cytosol + pOpen-deGFP (maxi +etOH) GFP-F-G35 0 days 00:32:16.243958277
Cytosol + pOpen-deGFP (maxi only) GFP-F-G35 0 days 00:32:40.052704496
Cytosol w/o DNA GFP-F-G35 0 days 03:29:05.730264123
PURExpress + pOpen-deGFP (maxi +etOH) GFP-F-G35 0 days 00:54:38.904421908
PURExpress + pOpen-deGFP (maxi only) GFP-F-G35 0 days 00:56:11.920378355
\
Data Max
Name Read
Cytosol + pOpen-deGFP (maxi +etOH) GFP-F-G35 24947.79 69624.69
Cytosol + pOpen-deGFP (maxi only) GFP-F-G35 27331.90 76261.25
Cytosol w/o DNA GFP-F-G35 262.36 63.86
PURExpress + pOpen-deGFP (maxi +etOH) GFP-F-G35 29285.52 43609.02
PURExpress + pOpen-deGFP (maxi only) GFP-F-G35 27094.04 38333.68
Lag \
Time
Name Read
Cytosol + pOpen-deGFP (maxi +etOH) GFP-F-G35 0 days 00:10:46.377326716
Cytosol + pOpen-deGFP (maxi only) GFP-F-G35 0 days 00:11:09.642098174
Cytosol w/o DNA GFP-F-G35 -1 days +23:22:35.625353708
PURExpress + pOpen-deGFP (maxi +etOH) GFP-F-G35 0 days 00:14:21.235910727
PURExpress + pOpen-deGFP (maxi only) GFP-F-G35 0 days 00:13:46.621002335
\
Data
Name Read
Cytosol + pOpen-deGFP (maxi +etOH) GFP-F-G35 4625.45
Cytosol + pOpen-deGFP (maxi only) GFP-F-G35 4912.16
Cytosol w/o DNA GFP-F-G35 78.34
PURExpress + pOpen-deGFP (maxi +etOH) GFP-F-G35 3323.52
PURExpress + pOpen-deGFP (maxi only) GFP-F-G35 2861.89
Steady State \
Time
Name Read
Cytosol + pOpen-deGFP (maxi +etOH) GFP-F-G35 0 days 01:03:55.210751325
Cytosol + pOpen-deGFP (maxi only) GFP-F-G35 0 days 01:04:19.820347956
Cytosol w/o DNA GFP-F-G35 0 days 09:32:00.010966036
PURExpress + pOpen-deGFP (maxi +etOH) GFP-F-G35 0 days 01:53:58.243123064
PURExpress + pOpen-deGFP (maxi only) GFP-F-G35 0 days 01:58:39.159726033
\
Data
Name Read
Cytosol + pOpen-deGFP (maxi +etOH) GFP-F-G35 47400.80
Cytosol + pOpen-deGFP (maxi only) GFP-F-G35 51930.60
Cytosol w/o DNA GFP-F-G35 498.48
PURExpress + pOpen-deGFP (maxi +etOH) GFP-F-G35 55642.48
PURExpress + pOpen-deGFP (maxi only) GFP-F-G35 51478.68
Fit \
params
Name Read
Cytosol + pOpen-deGFP (maxi +etOH) GFP-F-G35 [49895.57951478418, 5.582110894788535, 0.53784...
Cytosol + pOpen-deGFP (maxi only) GFP-F-G35 [54663.79376255666, 5.580083137013733, 0.54445...
Cytosol w/o DNA GFP-F-G35 [524.7139407465794, 0.4868169886601768, 3.4849...
PURExpress + pOpen-deGFP (maxi +etOH) GFP-F-G35 [58571.03311500861, 2.978292371722782, 0.91080...
PURExpress + pOpen-deGFP (maxi only) GFP-F-G35 [54188.08333108027, 2.8299959420167853, 0.9366...
R^2 drift
Name Read
Cytosol + pOpen-deGFP (maxi +etOH) GFP-F-G35 1.00 232.62
Cytosol + pOpen-deGFP (maxi only) GFP-F-G35 1.00 275.87
Cytosol w/o DNA GFP-F-G35 1.00 -25.33
PURExpress + pOpen-deGFP (maxi +etOH) GFP-F-G35 1.00 720.75
PURExpress + pOpen-deGFP (maxi only) GFP-F-G35 1.00 727.99 )
We can also calculate the kinetics and display the parameters as a table.
pr.kinetic_analysis(data)Loading...