Basic tracks

Abstract tracks

class pygv.tracks.track.Track(**kwargs: Any)

Generic Track

Parameters:

kwargs (dict) –

namestr

Name of the track

line_widthnumeric

The default width for lines

heightint

Height of the track (unit, relative measurement)

colorcolor_like

Default color, #A1A1A1

edge_colorcolor_like

Edge color, #6E6E6E

font_colorcolor_like

Font color, black

alphafloat

Alpha of patches

font_sizefloat

Font size

y_tick_formatstr

String format for ticks on y-axis. For example: {:.1f} (only keep one digit)

highlight_startint

Start loc of highlight region

highlight_endint

End loc of highlight region

highlight_colorcolor_like

Highlight color

highlight_alphafloat

Alpha for highlighting

y_label_rotationstr or float

Rotation of y-axis’ label, by default, vertical.

y_label_hastr

Horizontal alignment about label for y-axis

add_highlight_region(start, end)

Set highlight region

Parameters:

• start (numeric) – Start position of the highlight zone

• end (numeric) – End position of the highlight zone

property alpha

Alpha of patches

property color

Default color

property edge_color

Edge color

property font_color

Font color

property font_size

Font size

property height

Height of the track (unit, relative measurement)

property inward_yticks

Plot y-ticks strictly inside each track. If you want to apply inward_yticks to all tracks, you can set inward_yticks=True when creating the GenomeViewer, like GenomeViewer(inward_yticks=True)

Examples

(Source code, png, pdf)

property line_width

Line width

property name

Name of the track

remove_highlight()

Remove highlight zone

set_highlight_regions(starts, ends, colors=(), alpha_vals=())

Set highlight region

Parameters:

• starts (list of numeric values) – Start positions of the highlight zones

• ends (list of numeric values) – End positions of the highlight zones

• colors (tuple) – Leave it as an empty tuple if you want to use the default color. If you only give one color, it will be applied to all regions; otherwise, you should specify colors for each region.

• alpha_vals (tuple) – Leave it as an empty tuple if you want to use the default transparency level (0.5). If you only give one value, it will be applied to all regions; otherwise, you should specify transparency values for each region.

property y_label_ha

Set the horizontal alignment

property y_label_rotation

Rotation of y-axis’ label, by default, vertical.

property y_label_va

Set the vertical alignment

property y_tick_format

String format for ticks on y-axis

class pygv.tracks.track.AnnotationTrack(track, **kwargs)

Annotation track

Parameters:

• track (str)

• kwargs (dict) –

  allowed_feature_lanesNone or int

  allowed_feature_lanes

  heightfloat

  height

  arrow_interval :

  arrow_interval

  features_per_laneint

  features_per_lane

  font_box_alphafloat

  font_box_alpha

  lane_spacefloat

  lane_space

  line_color :

  line_color

  padding_leftint

  padding_left

  padding_rightint

  padding_right

  patch_heightint

  patch_height

  hide_visual_dupbool

  hide_visual_dup

property allowed_feature_lanes

Max amount of feature lanes to be plotted. For example, if a region has 12 overlapping features, to make sure all features can be clearly rendered, these features will be plotted into 12 separate lanes. If you set the value to be smaller than 12 (say 2), then you will only see two lanes in the end.

Examples

(Source code, png, pdf)

property arrow_interval

Intervals between arrows

property features_per_lane

Features per lane

property font_box_alpha

Transparent/alpha for text boxes labeling gene names

property height

Height of the track (unit, relative measurement)

property hide_visual_dup

Hide features which are “duplicates” to other features in current window (only one will be kept)

property lane_space

Extra spaces between lanes

property line_color

Line color

property padding_left

To ensure that feature names do not overlap with one another, you can introduce additional padding spaces on the left side of each feature. When setting an integer value (let’s call it \(x\)) for this property, features will be placed in separate lanes if the distance between them is less than x. Alternatively, if you opt for a float value between 0 and 1 (designated as \(f\)), the required spacing will be a fraction of the current visible region’s length (denoted as \(l\)), making the final spacing requirement equal to \(l\times f\).

property patch_height

Height of patches (for exons/blocks)

property show_name

By default, PyGV prints the names of genomic regions if available. This behavior can be changed by assigning False to this property.

class pygv.tracks.track.NumericalTrack(**kwargs)

Numerical track

Parameters:

kwargs (dict) –

max_valint, optional

Maximum value to be plotted. By default, all signals are plotted.

min_valint, optional

Minimum value to be plotted. By default, all signals are plotted.

label_masked_peakbool

Whether or not to labelled capped signals.

overflow_label_formatstr

String format for labeling overflow loci

overflow_label_auto_adjustbool

Switch controlling the automatic placement of text labels for overflow signals

property convert_nan_to_num

Nan conversion

property data_transform

Function for data transformation, currently supported values:

• None: no function will be called, return raw values

• “asinh”: inverse hyperbolic sine function

• “ln”: natural logarithm function (log base e)

• “log2”: the binary logarithm function (log base 2)

• “log10”: the common logarithmic function (log base 10)

• “log1p”: the natural logarithm of one plus (ln(1+x))

• function: a customized callable function

Note: If you add r at the beginning of log functions, values will be \(-f(-x)\)

Examples

(Source code, png, pdf)

property equal_space_for_pos_neg_ranges

Set it as True to force data range to be independently

property label_masked_peak

If the signal values are capped, setting this value as True will write the original values near the cap signs.

property max_val

Max value for the y-axis. If the signal values are greater than min_val, they will be capped.

property min_val

Min value for the y-axis. If the signal values are smaller than min_val, they will be capped.

property n_bins

Number of bins to apply, if a positive number is set, the window will be separated in bins and stat method will be applied, default None (raw signals)

property overflow_label_auto_adjust

Switch controlling the automatic placement of text labels for overflow signals

property overflow_label_format

String format for labeling overflow loci

reset_max_val()

Remove constraints for max value

reset_min_val()

Remove constraints for min value

property scale

Normalization factors for signals, you can set this value to normalize densities by RPM, etc.

property show_range

Max value for the y-axis

property stat_method

Statistical method for binning windows