`plasmidcanvas.plasmid`

Module Contents

Classes

Plasmid

Circular object representing a plasmid object on which to plot Features onto.

class plasmidcanvas.plasmid.Plasmid(name: str, base_pairs: int)

Circular object representing a plasmid object on which to plot Features onto.

Creates a Plasmid object with a given name and number of base pairs

Parameters:

name (str) – The name of the plasmid e.g. pBR322
base_pairs (int) – The number of base pairs in the plasmid

Raises:

ValueError – If the number of base pairs is negative

Examples

Creating a Plasmid:

from plasmidcanvas.plasmid import Plasmid
myplasmid = Plasmid("pBR322", 4361)

SUPPORTED_MARKER_STYLES = ['auto', 'n_markers', 'none']

SUPPORTED_TICK_STYLES = ['auto', 'none']

name: str

base_pairs: int

plot() → matplotlib.figure.Figure

Plots all features added to the Plasmid object onto a matplotlib Figure.

Note

Unless you are working in an interactive environment, e.g. Jupyter, it is recommended to use save_to_file() to view your plasmid instead.

Returns:: figure – A matplotlib figure object with the plasmid and its features plotted onto it
Return type:: Figure

Example

Obtaining a plasmid Figure:

from plasmidcanvas.plasmid import Plasmid
myplasmid = Plasmid("pBR322", 4361)
figure = myplasmid.plot()
proceed to view or work with figure...

save_to_file(filename: str) → None

Plots the plasmid by calling Plasmid.plot() and saves the figure to an image with a given filename.

Parameters:

filename (str) –

filename or path to save the figure to. e.g.: “myplasmid.png” would save it to the working directory. “build/myplasmid.png” would save the same image inside the “build” folder.

A file extention should be included in the filename. Any matplotlib supported file extention is supported. e.g. png, pdf, ps, eps and svg.

Examples

To save a plasmid to a png:

from plasmidcanvas.plasmid import Plasmid
myplasmid = Plasmid("pBR322", 4361)
myplasmid.savefig("figure.png")

add_feature(feature: plasmidcanvas.feature.Feature) → None

Adds a feature to the Plasmid object. All features to be plotted must be created and then added to the plasmid this way. See the example below.

Parameters:: feature (Feature) – A Feature object to add to the plasmid. e.g RectangleFeature, ArrowFeature, SinglePairLabel, RestrictionSite etc. See the documentation for plasmidcanvas.feature to see the availble Feature types and their usage.
Raises:: ValueError – If the feature lies out of bounds of the Plasmid’s base pair range

Note

This does not render the feature, that only happens when Plasmid.plot() or Plasmid.save_to_file() is ran. Therefore, plasmid wide and feature specific customisations can be made after the feature is added if you wish.

Examples

Adding an Arrow Featue:

from plasmidcanvas.plasmid import Plasmid
from plasmidcanvas.feature import ArrowFeature, RectangleFeature, RestrictionSite
myplasmid = Plasmid("pBR322", 4361)
myplasmid.savefig("figure.png")

arrow = ArrowFeature(1000, 2000)
# Optional feature customisation here
myplasmid.add_feature(arrow)

# Save plasmid out
myplasmid.save_to_file("figure.png")

get_features() → MutableSequence[plasmidcanvas.feature.Feature]

Get the features associated with the plasmid.

Returns:: features – The features associated with the plasmid.
Return type:: MutableSequence[Feature]

get_base_pairs() → int

Get the number of base pairs in the plasmid.

Returns:: base_pairs – The number of base pairs in the plasmid.
Return type:: int

set_base_pairs(base_pairs) → None

Set the number of base pairs in the plasmid.

Parameters:: base_pairs (int) – The number of base pairs to set the plasmid to.

get_name() → str

Get the name of the plasmid.

Returns:: name – The name of the plasmid.
Return type:: str

set_name(name: str) → None

Set the name of the plasmid.

Parameters:: name (str) – The name to set for the plasmid.

get_color() → str

Get the color of the plasmid circle.

Returns:: color – The color of the plasmid circle.
Return type:: str

set_color(color: str) → None

Set the color of the plasmid circle.

Parameters:: color (str) – The color to set for the plasmid circle. Use words e.g “red” or hex values e.g. “#FFFFFF”

get_center() → tuple[float, float]

Get the center coordinates of the plasmid.

Returns:: center – The (x, y) coordinates of the center of the plasmid.
Return type:: tuple[float, float]

set_center(center: tuple[float, float]) → None

Set the center coordinates of the plasmid.

Parameters:: center (tuple[float, float]) – The (x, y) coordinates to set as the center of the plasmid.

get_plasmid_line_width_sf() → float

Get the scale factor for the plasmid circle line width.

Returns:: line_width_sf – The scale factor for the plasmid circle line width.
Return type:: float

set_plasmid_line_width_sf(line_width_sf: float) → None

Set the scale factor for the plasmid circle line width.

Parameters:: line_width_sf (float) – The scale factor to set for the plasmid circle line width. e.g. 1.5 makes the plasmid circle 1.5 times as thick as the default

get_plasmid_line_width() → float

Get the plasmid line width.

Returns:: plasmid_line_width – The plasmid line width.
Return type:: float

set_plasmid_line_width(plasmid_line_width: float) → None

Set the plasmid line width.

Parameters:: plasmid_line_width (float) – The plasmid line width to set.

Note

Either use set_plasmid_line_width or set_plasmid_line_width_sf. Increasing both values could create a very thick plasmid circle!

get_marker_style() → str

Get the style of markers for the plasmid.

Returns:: marker_style – The style of markers used for the plasmid.
Return type:: str

set_marker_style(marker_style: str) → None

Set the style of markers for the plasmid.

Parameters:: marker_style (str) – The style of markers to set for the plasmid. Currently supported styles

“auto” (default) - Automatically apply markers at a reasonable marker interval based on the plasmid size

“n_markers” - Place n equidistant markers around the circle. The default is 16, unless changed with Plasmid.set_number_of_markers()

“none” - No markers added to the circle
Raises:: ValueError – If the given marker_style is not in Plasmid.SUPPORTED_MARKER_STYLES, as listed above.

get_marker_distance_sf() → float

Get the scale factor for the distance between the circle and the marker text.

Returns:: marker_distance_sf – The scale factor for the marker distance.
Return type:: float

set_marker_distance_sf(marker_distance_sf) → None

Set the scale factor for the distance between the circle and the marker text.

Parameters:: marker_distance_sf (float) – The scale factor to set for the marker distance.

Examples

This value is small by default (1.03). It is advised to alter this by applying a to the existing scale factor to achieve reliable increases.:

myplasmid.set_marker_distance(myplasmid.get_marker_distance_sf() * 1.5)

get_number_of_markers() → int

Get the number of markers on the plasmid. Only used when the plasmid’s marker style is “n_markers”.

Returns:: number_of_markers – The number of markers on the plasmid.
Return type:: int

set_number_of_markers(number_of_markers: int) → None

Set the number of markers to produce around the plasmid when the plasmid’s marker style is “n_markers”.

Parameters:: number_of_markers (int) – The number of markers to place around the plasmid when using n_marker style.

get_tick_style() → str

Get the style of tick placement on the plasmid.

Returns:: tick_style – The style of ticks used for the plasmid.
Return type:: str

set_tick_style(tick_style: str) → None

Set the style of tick placement on the plasmid.

Parameters:

tick_style (str) – The style of ticks to set for the plasmid.

Currently supported:

“auto” (default) - Automatically draw on ticks at a reasonable marker interval based on the plasmid size

“none” - No ticks are drawn around the circle

Raises:

ValueError – If the given tick_style is not in Plasmid.SUPPORTED_TICK_STYLES, as listed above.

get_tick_color() → str

Get the color of ticks for the plasmid.

Returns:: tick_color – The color of ticks used for the plasmid.
Return type:: str

set_tick_color(tick_color: str) → None

Set the color of ticks for the plasmid.

Parameters:: tick_color (str) – The color of ticks to set for the plasmid. Use words e.g “red” or hex values e.g. “#FFFFFF”

get_feature_label_font_size() → int

Get the override font size of feature labels for the plasmid. This font size will be applied to any labels / features that have not already had their font size changed manually.

Returns:: feature_label_font_size – The font size of feature labels used for the plasmid. Given as a pt value.
Return type:: int

set_feature_label_font_size(feature_label_font_size: int) → None

Set the font size of feature labels for the plasmid. This font size will be applied to any labels / features that have not already had their font size changed manually.

Parameters:: feature_label_font_size (int) – The font size of feature labels to set for the plasmid. Given as a pt value.

plasmidcanvas.plasmid

Module Contents

Classes

`plasmidcanvas.plasmid`