Bandwagon Reference manual¶

Ladders utilities¶

Definition of custom ladders for BandWagon.

bandwagon.ladders.custom_ladder(label, bands_migrations)[source]¶

Generate a BandsPattern object meant to be used as a ladder.

By default the ladder is dark red on a white background.

bandwagon.ladders.ladder_from_aati_fa_calibration_table(filepath=None, dataframe=None, label=None)[source]¶

Extract a BandPattern from an AATI Fragment Analyzer calibration file.

The calibration table is generated after each run from the migration times of the ladder and is generally in a file called something like 2016 11 08 16H 57M Size Calibration.csv.

This method requires Pandas installed.

Parameters

filepath: Path to the calibration file.
dataframe: Pandas dataframe obtained by reading the file, can be provided instead of filepath.
label: Label that will be given to the ladder when plotted.

BandsPatternsSet¶

Define Bandwagon’s classes Band, BandPattern, BandsPatternsSet.

class bandwagon.BandsPatternsSet.BandsPatternsSet(patterns, ladder, label=None, label_fontdict=None, global_patterns_props=None, ladder_ticks=None, ticks_fontdict=None, alternate_background_colors='#e2edff', '#fffae2')[source]¶

A set of band patterns, that will be plotted next to one another.

Parameters

patterns: A list of patterns, in the order in which they will be displayed. Each pattern can be either a BandPattern object or a list of Band objects or a list of DNA sizes.
ladder: A BandsPattern to use as a ladder.
label: A label that will be displayed vertically on the left of the final plot.
label_fontdict: Font dictionary for the label e.g. {‘color’: ‘red’, ‘size’: 7}.
global_patterns_props: Properties that override that of each pattern in the set.
ladder_ticks: List of DNA sizes that will be represented by ticks on the left of the plot to guide the reading.
ticks_fontdict: Font dictionnary for the ticks indicating dna sizes.
alternate_background_colors: Colors that will be alternated for the backgrounds of the different columns. Leave to None for no background. If some patterns have a background color set this color will override the alternate_background_colors.

plot(ax=None)[source]¶: Plot the band patterns on the given Matplotlib ax.

plot_with_bokeh(max_visible_patterns=12, band_width_pixels=40)[source]¶

Return an interactive (browser-based) Bokeh figure of the patterns.

Parameters

max_visible_patterns: Max number of patterns that will be visible at the same time. A horizontal scroll will allow to see more patterns if there are more
band_width_pixels: Size of a band width in pixels on the screen. Said otherwise, the final figure will have a width of band_width_pixels * visible

BandsPattern¶

Define Bandwagon’s classes Band, BandPattern, BandsPatternsSet.

class bandwagon.BandsPattern.BandsPattern(bands, ladder=None, label=None, label_fontdict=None, corner_note=None, corner_note_fontdict=None, topology=None, background_color=None, width=1.0, global_bands_props=None, gel_image=None, gel_image_width=0.2, band_is_uncut=False)[source]¶

Bands set forming a migration pattern. Also used to define ladders.

Parameters

bands: Either a list of Band objects, or a list of DNA sizes e.g. [800, 654, 1752]. In the latter case, a ladder must be provided to determine the elements.
ladder: A BandsPattern to use as a ladder in case bands is a list of DNA sizes. Else leave it to None.
label: Label to be printed on top of the band pattern.
label_fontdict: A dict indicating the format of the label if any provided. For instance {'size': 7, 'rotation':30, 'color': '#0011aa'}.
corner_note: Note to be printed in small prints in the corner of the band lane. Useful to print e.g. the total sum of all bands, or some remark.
corner_note_fontdict: A dict indicating the format of the label if any provided. For instance {'size': 6, 'color': '#0011aa'}.
topology: Another type of (top-right) corner note, either “circular” or “linear”.
background_color: Background color of the column in which the pattern is plotted. Either the name of a color or a html code (‘#0012e4’).
width: Width of the column (better keep to 1.0 if you want my humble opinion)
global_bands_props: Dictionary of band properties overwriting that of all bands in the pattern, e.g. {'color': '#012ff45'}.
gel_image: A numpy array of size w x h and values in 0-1 representing a gel image. This image will be superimposed on the right of the pattern’s color.
gel_image_width: Width of the gel_image display (remember that the width of the column is 1.0, so 0.2 means this ‘photo’ will occupy 1/5 of the column, the rest being occupied by the pattern plot).
band_is_uncut: If True, a “UNCUT” message will be added under the single band.

dna_size_to_migration(dna_sizes)[source]¶: Return the migration distances for the given dna sizes.

initialize()[source]¶

Create the variables necessary to compute some properties.

Concerned properties are self.dna_sizes, self.migration_distances, self.migration_distances_span, self.dna_size_span, and indirectly the functions dna_size_to_migration and migration_to_dna_size.

merge_with(other)[source]¶: Merge this band pattern with another pattern’s bands.

migration_to_dna_size(migration_distances)[source]¶: Return the dna sizes corresponding to the given migrations.

modified(**attributes)[source]¶: Return a version of this bands pattern with modified attributes.

plot(ax, x_coord)[source]¶: Plot background, bands, label, gel_image at the given x_coord.

Band¶

class bandwagon.Band.Band(dna_size, migration_distance=None, ladder=None, band_color='#000000', band_thickness=2, band_width=0.7, label=None, label_fontdict=None, html=None)[source]¶

A band in a migration pattern.

This class controls all visual aspects of the band (form, color, label…).

Parameters

dna_size
migration_distance: Observed migration distance of the band. Useful if you are using this band to define a ladder, otherwise keep to None.
ladder: Ladder used to determine the migration distance of the band, if no migration_distance was provided.
band_color: Color of the band. Can be a color name (like ‘black’, ‘red’…) or an hexadecimal code like ‘#001aff’ (this format is mandatory if you want to export to browser-based display.
band_thickness: Thickness of the band in pixels.
band_width: Proportion of the column width that is occupied by the band (the columns for each band pattern have a width of 1.0).
label: Label to be printed on the band, if any provided. Set to ‘=size’ for printing the band sizes.
label_fontdict: A dict indicating the format of the label if any provided. For instance {'size': 7, 'weight':'bold', 'color': '#0011aa'}.
html: Html appearing when hovering the band.

modified(**attributes)[source]¶: Return a new version of this band, with modified attributes.

plot(ax, x_coord)[source]¶: Plot the band’s line and label on the ax at the x-coordinate.

to_json(ladder=None)[source]¶: Return a dictionary version of the band (for bokeh plotting).

Plots¶

class bandwagon.plot_records_digestions.DigestGraphicTranslator(features_filters=(), features_properties=None)[source]¶

compute_feature_color(feature)[source]¶

Compute a color for this feature.

If the feature has a color qualifier it will be used. Otherwise, the classe’s default_feature_color is used.

To change the behaviour, create a subclass of BiopythonTranslator and overwrite this method.

bandwagon.plot_records_digestions.annotate_digestion_bands(record, enzymes, ladder)[source]¶: Annotate the record to indicate the regions corresponding to bands.

bandwagon.plot_records_digestions.plot_all_digestion_patterns(records, digestions, ladder, axes=None, group_by='digestions', show_band_sizes=False, plot_ladder=False)[source]¶

Plot a grid (RECORD x DIGESTION) of predicted records digestions.

Parameters

records: List of biopython records whose digests need to be digested by the digestions.
digestions: List of tuples of enzyme names e.g. [('BsaI',),`('MfeI', 'BsmBI')...] representing the digestions for the provided records.
ladder: A Ladder object representing the ladder to be used for placing the bands
axes.: If None, new axes will be created.
group_by: Either “sequence” or “digestion”. Determines the plotting order.
show_band_sizes: If true, the band sizes will be printed on each band.

bandwagon.plot_records_digestions.plot_record_digestion(record_digestion, ladder, record_label, digestion_label)[source]¶

Plot the digestion along with a schema of cuts locations in the record.

Parameters

record_digestion: Biopython record with features indicating bands.
ladder
record_label: Label to use as the title of the record digestion plot.
digestion_label: Label to use as the title of the bands pattern(s).

bandwagon.plot_records_digestions.plot_records_digestions(target, ladder, records_and_digestions=None, records=None, digestions=None)[source]¶

Plot records digestions in a multipage PDF file.

Parameters

records_and_digestions: A list [(record, digestion), …] where record is a Genbank record and digestions a tuple of enzymes. Alternatively, a list of records and digestions can be provided.
records: List of biopython records whose digests need to be digested by the digestions.
digestions: List of tuples of enzyme names e.g. [('BsaI',),`('MfeI', 'BsmBI')...] representing the digestions for the provided records.
ladder: A Ladder object representing the ladder to be used for placing the bands.
target: path to a PDF file, or file-like object.
full_report