Plotting Customisation

Plotting Data

All examples use these data unless specified otherwise:

from plotprofile import ReactionProfilePlotter

energy_sets = {
    "Pathway A": [0.0, -2.0, 10.0, 1.5, -1.5, 2.0, -7.0],
    "Pathway B": [None, -2.0, 6.0, 4.0, 5.0, 2.0, None]
}

Parameters

This table summarizes the main plotting style parameters.

Parameter	Default	Description
figsize	[5, 4.5]	Figure size in inches (width, height)
point_type	hollow	Marker type for points (hollow, dot, bar, etc.)
curviness	0.42	Controls how curved the lines are
desaturate	True	Whether to desaturate colors
dashed	[]	List of lines to render as dashed
line_width	2.5	Width of line plots
bar_width	3.0	Width of bars if using bar points
show_legend	True	Display the legend
colors	[“darkcyan”, …]	List of colors for lines
annotation_color	maroon	Color for annotations
energy	G	Type of energy plotted (G, H, E, etc.)
units	kcal	Units of energy

Examples

1. Axes Display

Axes can be shown selectively using the axes parameter:

• axes='y' shows only the y-axis.

• axes='x' shows only the x-axis.

• axes='both' shows both axes.

• axes='box' shows 4 axes.

• axes=None hides both axes.

plotter = ReactionProfilePlotter(axes='y')
plotter.plot(energy_sets, filename="../images/profile13")

Parameter	Value
axes	y

2. Axis Labels and Units

Axis labels can be fully customized:

• x_label and y_label, which override the labels completely.

• energy can be e|electronic|g|gibbs|h|enthalpy|s|entropy to automatically label the y-axis.

• units sets the y-axis units: ‘kcal’ or ‘kj’.

plotter = ReactionProfilePlotter(
    energy='E',
    units='kcal',
    x_label='Reaction',
)
plotter.plot(energy_sets, filename="../images/profile14")

Parameter	Value
x_label	Reaction
energy	E
units	kcal

3. Legend Options

The legend can be turned on/off, and specific lines can be included or excluded:

• show_legend toggles visibility. Default is True. This is controlled in the class as a global parameter.

• exclude_from_legend hides specific lines. This is a plot function parameter.

• include_keys ensures certain keys are plotted even if not in the energy list. This is also a plot function parameter.

energy_sets = {
    "Pathway A": [0.0, -2.0, 10.0, 1.5, -1.5, 2.0, -7.0],
    "Pathway B": [None, -2.0, 6.0, 4.0, 5.0, 2.0, None],
    "Pathway C": [None, None, 3.0, 5.0, 6.0, 1.0, -2.0],
}
plotter = ReactionProfilePlotter(
    show_legend=True,
)
plotter.plot(energy_sets, exclude_from_legend=['Pathway A'], include_keys=["Pathway A", "Pathway C"], filename="../images/profile15")

Parameter	Value
show_legend	True
exclude_from_legend	[‘Pathway B’]
include_keys	[‘Pathway A’, ‘Pathway C’]

4. Point Types

Point styles can be selected with point_type:

• Options: ‘hollow’, ‘dot’, ‘bar’.

plotter = ReactionProfilePlotter(point_type='dot')
plotter.plot(energy_sets, filename="../images/profile16")

Parameter	Value
point_type	dot

5. Bar Plot Customization

Bars have additional options:

• bar_length and bar_width control size.

• connect_bar_ends determines if lines connect to the bar center or ends.

  • Default is True

plotter = ReactionProfilePlotter(
    point_type='bar',
    bar_length=0.8,
    bar_width=0.3,
    connect_bar_ends=True
)
plotter.plot(energy_sets, filename="../images/profile17")

Parameter	Value
point_type	bar
bar_length	0.8
bar_width	0.3
connect_bar_ends	True

6. Dashed Lines

Lines can be dashed selectively with the dashed parameter

• Pass a list of keys to make those lines dashed.

• dash spacing can be controlled with dash_spacing (default is 2.5).

plotter = ReactionProfilePlotter(dashed=['Pathway A'])
plotter.plot(energy_sets, filename="../images/profile18")

Parameter	Value
dashed	[‘Pathway A’]
dash_spacing	2.5

7. Line Curviness

The curviness parameter uses Bezier curves to control line curvature:

• 0.0 → straight lines

• 0.0–1.0 → increasing curvature

plotter = ReactionProfilePlotter(curviness=0.7)
plotter.plot(energy_sets, filename="../images/profile19")

Parameter	Value
curviness	0.7

8. Colors

Colors can be customized:

• Pass a list of named colors (will cycle if fewer than energy sets, truncate if longer).

• Alternatively, pass a string of a colormap i.e. ‘viridis’, ‘plasma’, ‘blues’, ‘reds_r’, etc.

plotter = ReactionProfilePlotter(
    .. colors=['red','green','blue'],
    colors='Reds_r'
)
plotter.plot(energy_sets, filename="../images/profile20")

Parameter	Value
colors | Reds_r

9. Saturation

By default, the color of the lines are desaturated slightly relative to the points. This can be turned off with the desaturate parameter.

• This can also be controlled with desaturate-factor which is a float from 1.0 where this is the original increasing to increase desaturation.

  • default is 1.2

plotter = ReactionProfilePlotter(desaturate=False)
plotter.plot(energy_sets, filename="../images/profile21")

Parameter	Value
desaturate	False

10. Annotations

Annotations can be added to the plot using the annotations parameter in the format:

dict{ ‘Annotation’: (start_index, end_index) }

This adds an arrow at the bottom, with the text centered on the arrow.

• The arrow color can be set with arrow_color.

• The annotation text color can be set with annotation_color.

• The annotation text size can be set with annotation_size.

• Additional options include annotation_below_arrow to place the text below the arrow instead on on the arrow.

annotations = {
    "A": (0, 1),
    "B": (2, 3),
    "C": (4, 5)
}
plotter = ReactionProfilePlotter()
plotter.plot(energy_sets, annotations=annotations, filename="../images/profile22")

Parameter	Value
annotations	{‘A’: (0, 1), ‘B’: (2, 3), ‘C’: (4, 5)}
arrow_color	xkcd:dark grey
annotation_color	maroon
annotation_size	11

11. Labels

Labels of points can be added in the following way:

• Pass a dict(list) of strings to the point_labels parameter.

• The keys are the energy set names, and the values are lists of labels for each point.

point_labels = {
    "Pathway A": ["Int1", "Int2", "TS1", "Int3"],
    "Pathway B": [None, None, "TS2" ]
}
plotter = ReactionProfilePlotter(point_labels=point_labels)
plotter.plot(energy_sets, point_labels=point_labels, filename="../images/profile23")

Parameter	Value
point_labels	{‘Pathway A’: [None, ‘TS1’, ‘Int1’, ‘TS2’]}