plotprofile

plotProfile

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

Installation

Google Colab

Can be used with colab.ipynb without a local install

From pypi

Simplest installation

pip install plotprofile

Local installation

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

[!WARNING] this may not respect the styles.json, if not:

git clone [e-mail]:aligfellow/plotProfile.git
cd plotProfile
python -m build
pip install dist/plotprofile*tar.gz

Python Usage examples

Example 1

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, None, -2.0],
    "diastereomer": [None, None, 12.2],
    "diastereomer2": [None, None, 9.8, 9.8]
}
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")

Passing in annotations for labelling of the reaction profile:

• this is done in the plotting function rather than the class
• using dictionary with keys of labels and a tuple of the start and end x-indices
• allowing for multiple plots of the same style with different annotations

Example 2

A variety of other 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
  • if the colour list is too short then colours will be repeated.
  • if the cmap is invalid, viridis will be set as a default
• show_legend=Bool
• units="kj|kcal"
• energy="e|electronic|g|gibbs|h|enthalpy|s|entropy|"
• x_label and y_label can be used to set cutoms axis labels

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

plotter = ReactionProfilePlotter(style="presentation", dashed=["Pathway B"], point_type='dot', desaturate=False, colors='Blues_r', show_legend=False, curviness=0.5, x_label='Reaction Profile', y_label='Free Energy (kcal/mol)')
plotter.plot(energy_sets, filename="../images/profile2")

Example 3

• Straight lines set in a style, which can also be done by passing in curviness=0
• Labels can be placed below the annotation arrow
• Some parameters regarding the plotting data can be tuned in ReactionProfilePlotter.plot:
  • include_keys - only some of the energy_sets keys() included in the plot
  • exclude_from_legend - excluded one of the energy_sets key from the legend

plotter = ReactionProfilePlotter(style="straight", figsize=(6,4), dashed=["Pathway C"], point_type='bar', annotation_color='black', axes='y', colors=['midnightblue', 'slateblue', 'darkviolet'], energy='electronic', units='kj', annotation_below_arrow=True, dash_spacing=5.0, desaturate=False)
plotter.plot(energy_sets, annotations=annotations, filename="../images/profile3", exclude_from_legend=["Pathway B"], include_keys=["Pathway A", "Pathway B", "Pathway C", "diastereomer"])

Example 4

• Point labels can be also added by passing point_labels to ReactionProfilePlotter.plot
• Annotations can accomodatenewline characters \n and spacing will be adjusted automatically

from plotProfile import ReactionProfilePlotter

energy_sets = {
    "1": [-3.0, 12.5, 2.9, 0.0, 1.8, 10.5, 2.9]
}

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

point_labels = {
    "1": [None, "TS1", None, "Int1", None, "TS2"]
}

plotter = ReactionProfilePlotter(figsize=(4.5,4), axes='box', show_legend=False)
plotter.plot(energy_sets, annotations=annotations, point_labels=point_labels, filename="../images/profile4")

Example 5

• Bar lengths and widths can be adjusted
• Default line/curve behaviour with bars is to connect at the edges, this can be turned off with connect_bar_ends=False
• Dash spacing of the line can be changed with dash_spacing

from plotProfile import ReactionProfilePlotter

energy_sets = {
    "1": [-3.0, 12.5, 2.9, 0.0, 1.8, 10.5, 2.9]
}

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

point_labels = {
    "1": [None, "TS1", None, "Int1", None, "TS2"]
}

plotter = ReactionProfilePlotter(figsize=(4.5,4), axes='box', curviness=0.5, show_legend=False, point_type='bar', bar_length=0.3, bar_width=3, connect_bar_ends=False, dashed=["1"], dash_spacing=1.5)
plotter.plot(energy_sets, annotations=annotations, point_labels=point_labels, filename="../images/profile5")

See examples/example.ipynb

Further details

[!IMPORTANT]

• Secondary curves can begin from after the 1st point, just need to have a None entry in the list of energies e.g. [None, 0.0, 1.0]
• Individual points can be placed if this is a list with only one energy value (e.g. uncluttered diastereomeric TS for example, see examples)
  • labels of theses are not added to the legend
  • these can even be placed as individual points between two indices with [None, 5.0, 5.0]
• Spacing of points on the profile can be altered by:
  • passing the same energy twice in a row, which will place the point halfway between the two x-indices, i.e. Pathway C point in examples, e.g. [0.0, 5.0, 5.0]
  • with an entry like [0.0, None, 1.0] which will have a line connecting indexes 0 and 2 of this list with the correct x-axis alignment
• data types can be:
  • dict, with labels for the legend
  • list of lists (no labelling of different profiles)
  • single list

CLI

[!NOTE] Currently untested - though this won't work for now

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

To Do

[!TIP]

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

Configuration options

The behavior can be customized via styles.json or by passing parameters to ReactionProfilePlotter(). Here are all available options from styles.json:

{
    "default": {
      "figsize": [5,4.5],
      "point_type": "hollow",
      "curviness": 0.42,
      "desaturate": true,
      "desaturate_factor": 1.2,
      "dashed": [],
      "dashed_spacing": 2.5,
      "labels": true,
      "show_legend": true,
      "line_width": 2.5,
      "bar_width": 3.0,
      "bar_length": 0.3,
      "marker_size": 6,
      "font_size": 10,
      "font_family": "Arial",
      "font_weight": "bold",
      "font_style": "normal",
      "axis_linewidth": 2.0,
      "buffer_factor": 0.05,
      "axes": "box",
      "colors": ["darkcyan", "maroon", "midnightblue", "darkmagenta", "darkgreen", "saddlebrown"],
      "segment_annotations": [],
      "arrow_color": "xkcd:dark grey",
      "annotation_color": "maroon",
      "annotation_size": 10,
      "energy": "G",
      "units": "kcal",
      "annotation_below_arrow": false,
      "annotation_space": 0.05,
      "annotation_buffer": 0.0,
      "arrow_width": 1.5,
      "sig_figs": 1,
      "point_label_color": "black",
      "connect_bar_ends": true
    },
    "presentation": {
      "figsize": [8, 5],
      "font_size": 14,
      "annotation_size": 14,
      "marker_size": 8,
      "line_width": 3.0,
      "bar_width": 3.5,
      "annotation_space": 0.12,
      "arrow_width": 2.5
    },
    "straight": {
      "curviness": 0.0
    }
  }