An interactive Jupyter notebook to plot chromatograms outputted from GE Life Sciences / Amersham Biosciences UNICORN 5.X software. To use this notebook, simply output an .XLS file from the UNICORN software, containing all curves / traces (i.e. UV absorbance, conductivity, Temperature, etc.). Save this file in the same directory as the .ipynb file for this notebook, and re-run the cells.
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%matplotlib inline
from fplcplot.chromatogram import plotTraces
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file_list = !ls *A.xls
file_list
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To plot your figure, simply run the below cell to generate a series of iPython widgets as interface to FPLCPlot. Any changes made to the parameters on the plot are shown after pressing the Run plotTraces button. (Note: Interactive widgets are not visible in online notebook viewers such as on GitHub. Launch this notebook locally to view the widgets.)
| Name | Description |
|---|---|
| Title | Title for figure. Latex supported by enclosing in $$ |
| Save file? | Check to save file in same directory. File name is according to first Excel file used in plotting figure. |
| File format | File format for outputted file. .PNG or .PDF supported. |
| Lower y-limit | Lower limit on y-axis for UV absorption trace |
| Upper y-limit | Upper limit on y-axis for UV absorption trace |
| 2nd trace | Choice for plotting curve on second y-axis. buffer_b plots the percentage of buffer B on the second y-axis buffer_b_abs plots the actual concentration resulting from mixture of buffer A and B (This requires correct values in the buffer B sliders below). conductivity plots the percentage conductivity on the second y-axis. |
| *Buffer A (mM) | The absolute value in concentration for competitor in buffer A in mM. |
| *Buffer B (mM) | The absolute value in concentration for competitor in buffer B in mM. |
*Note: Values for Buffer A and Buffer B must be correct when plotting using the buffer_b_abs setting, as these values are used to calculate the actual concentration of the competitor in solution (e.g. imidazole).
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from ipywidgets import interact, interactive, fixed
import ipywidgets as widgets
from IPython.display import display
interact(plotTraces, file_list=fixed(file_list),
title=widgets.Text("Protein A $E. coli$", description='Title:'),
output=widgets.Checkbox(value=False, description="Save file?"),
f_format=widgets.Dropdown(options=['.png', '.pdf'], description='File format:'),
y_lower=widgets.IntSlider(min=-200,max=100,step=10,value=-20,
description='Lower y-limit:'),
y_upper=widgets.IntSlider(min=-10,max=4500,step=50,value=2000,
description='Upper y-limit:'),
second_trace=widgets.ToggleButtons(options=['None','buffer_b',
'buffer_b_abs',
'conductivity'],
description='2nd trace:'),
buffer_A=widgets.IntSlider(min=0,max=500,step=10,value=10,
description='Buffer A (mM):'),
buffer_B=widgets.IntSlider(min=0,max=3000,step=10,value=400,
description='Buffer B (mM):'),
__manual=True)
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