# Quickstart

## Example 1

```python
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(linestyle={"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

```{image} ./images/profile1.png
:height: 300
:alt: Example 1
```

## Example 2

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

```python
plotter = ReactionProfilePlotter(style="presentation", linestyle={"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")
```

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, **superceeding** `units` or `energy`

```{image} ./images/profile2.png
:height: 300
:alt: Example 2
```

## Example 3

```python
plotter = ReactionProfilePlotter(style="straight", figsize=(6,4), linestyle={"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"])
```

- 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

```{image} ./images/profile3.png
:height: 300
:alt: Example 3
```

## Example 4

```python
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")
```

- Point labels can be also added by passing `point_labels` to `ReactionProfilePlotter.plot`

- Annotations can accommodate newline characters `\n` and spacing will be adjusted automatically

```{image} ./images/profile4.png
:height: 300
:alt: Example 4
```

## Example 5

```python
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, linestyle={"1": "--"}, dash_spacing=1.5)
plotter.plot(energy_sets, annotations=annotations, point_labels=point_labels, filename="../images/profile5")
```

- 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`

```{image} ./images/profile5.png
:height: 300
:alt: Example 5
```

## Saving

Plots can be saved by passing `filename` to `plotter.plot()`. The output format is controlled by `file_format` and supports any standard matplotlib format (e.g. `png`, `svg`, `pdf`, `eps`). Resolution can be set with `dpi` (default: 600).

```python
plotter.plot(energy_sets, filename="my_profile", file_format="svg", dpi=300)
```