plotprofile 1.0.1

Plot reaction profiles with customizable curves and labels

plotProfile

Python code for plotting professional looking reaction profiles with various customisation options available

Installation

Local installation (may not respect the styles.json):

git clone [e-mail]:aligfellow/plotProfile.git
cd plotProfile
pip install .

From pypi

pip install plotprofile

Python Usage examples

Use case for example:

from plotProfile import ReactionProfilePlotter

energy_sets = {
    "Pathway A": [0.00, -2.0, 10.2, 1.4, -1.5, 2.0, -7.2],
    "Pathway B": [None, -2.0, 6.2, 4.3, 5.8, 2.0],
    "Pathway C": [None, -2.0, -6.8,-6.8],
}

annotations = {
    'Step 1': (0,3),
    'Step 2': (3,5),
    'Step 3': (5,6),
}

plotter = ReactionProfilePlotter(dashed=["Pathway C"])
plotter.plot(energy_sets, annotations=annotations, filename="../images/profile1")

Pass in annotations for labelling of the reaction profile:

• this is done in the plotting function rather than the class
• allowing for multiple plots of the same style with different annotations

A variety of paremters can be tuned for the plotting, including:

• axes="box|y|x|both|None"
• curviness=0.42 - reduce for less curve and vice versa
• colors=["list","of","colors"]|cmap - specify colour list or colour map
• show_legend=Bool
• units="kj|kcal"
• energy="e|electronic|g|gibbs|h|enthalpy|s|entropy|"

For example:

plotter = ReactionProfilePlotter(style="presentation", dashed=["Pathway B"], point_type='bar', desaturate=False, colors='Blues_r', show_legend=False, curviness=0.5)
plotter.plot(energy_sets, filename="../images/profile2")

Using style="presentation" which sets a larger figsize=(X,X), thicker lines, larger font size:

For example:

plotter = ReactionProfilePlotter(style="straight", figsize=(6,4), dashed=["Pathway C"], point_type='dot', annotation_color='black', axes='y', colors=['darkseagreen', 'slateblue', 'darksalmon'], energy='electronic', units='kj')
plotter.plot(energy_sets,annotations=annotations, filename="../images/profile3")

Straight lines set in a style, which can also be done by passing in curviness=0:

See examples/example.ipynb for more explicit code

Further details

• Secondary curves can begin from after the 1st point, just need to have a None entry in the list of energies
• Spacing of energies can be altered by passing the same energy twice in a row
  • this will place the point halfway between the two x indices,
    • i.e. Pathway C point in examples

CLI - to do...

Currently untested - probably won't work for now

python -m plotProfile --input examples/input.json --labels --format png

To Do

• label placement is primitive and could be improved
  • for now these can be tweaked with postprocessing
• check cli options