glyphs
Contains the Glyph class used to define the different type of glyphs that can be used to represent features, as well the basic plotting functions for GenomeBrowser
Glyph
Glyph (glyph_type:str='arrow', colors:tuple=('purple', 'orange'), alpha:float=0.8, show_name:bool=True, height:float=1)
A class used to define the different types of glyphs shown for different feature types.
| Type | Default | Details | |
|---|---|---|---|
| glyph_type | str | arrow | type of the Glyph (arrow or box) |
| colors | tuple | (‘purple’, ‘orange’) | can be a single color or a tuple of two colors, one for each strand |
| alpha | float | 0.8 | transparency |
| show_name | bool | True | |
| height | float | 1 | height of the feature relative to other features (between 0 and 1) |
get_default_glyphs
get_default_glyphs ()
Returns a dictionnary with:
- keys: feature types (str)
- values: a Glyph object
default_glyphs['CDS']Glyph object with attributes:
glyph_type: arrow
colors: ('purple', 'orange')
height: 1
alpha: 0.8
show_name: Trueget_patch_coordinates
get_patch_coordinates (feature, glyphs_dict, feature_height=0.15)
data_path = get_example_data_dir()
gff_path = os.path.join(data_path, "MG1655_U00096.gff3")
features=parse_gff(gff_path,
feature_types=default_types,
seq_id="U00096.3")
features.head().apply(get_patch_coordinates,glyphs_dict=default_glyphs, axis=1)0 (((190, 190, 190, 255, 190), (0.05, 0.2, 0.2, ...
1 (((337, 337, 2699, 2799, 2699), (0.05, 0.2, 0....
2 (((2801, 2801, 3633, 3733, 3633), (0.05, 0.2, ...
3 (((3734, 3734, 4920, 5020, 4920), (0.05, 0.2, ...
4 (((5234, 5234, 5430, 5530, 5430), (0.05, 0.2, ...
dtype: objectget_feature_name
get_feature_name (feature, glyphs_dict, name='gene', attributes:list=['gene', 'locus_tag', 'product'])
Gets the name of the feature to be displayed. If the Glyph for the feature type has the attribute show_name=False then an empty string is returned. If name is not an attribute of the feature, then the first attribute in the attributes list is used.
features.head().apply(get_feature_name,name="gene",glyphs_dict=default_glyphs, axis=1)0 thrL
1 thrA
2 thrB
3 thrC
4 yaaX
dtype: objectget_feature_patches
get_feature_patches (features:pandas.core.frame.DataFrame, left:int, right:int, glyphs_dict:dict, attributes:list=['gene', 'locus_tag', 'product'], name:str='gene', feature_height:float=0.15)
| Type | Default | Details | |
|---|---|---|---|
| features | DataFrame | DataFrame of the features | |
| left | int | left limit | |
| right | int | right limit | |
| glyphs_dict | dict | a dictionnary of glyphs to use for each feature type | |
| attributes | list | [‘gene’, ‘locus_tag’, ‘product’] | list of attributes to display when hovering |
| name | str | gene | attribute to be displayed as the feature name |
| feature_height | float | 0.15 | fraction of the annotation track height occupied by the features |
| Returns | DataFrame |
get_feature_patches(features,8000,12000, glyphs_dict=default_glyphs, name="gene")| names | xs | ys | color | alpha | pos | gene | locus_tag | product | |
|---|---|---|---|---|---|---|---|---|---|
| 0 | talB | (8238, 8238, 9091, 9191, 9091) | (0.05, 0.2, 0.2, 0.125, 0.05) | purple | 0.8 | 8714.5 | talB | b0008 | transaldolase B |
| 1 | mog | (9306, 9306, 9793, 9893, 9793) | (0.05, 0.2, 0.2, 0.125, 0.05) | purple | 0.8 | 9599.5 | mog | b0009 | molybdopterin adenylyltransferase |
| 2 | satP | (10494, 10494, 10028, 9928, 10028) | (0.05, 0.2, 0.2, 0.125, 0.05) | orange | 0.8 | 10211.0 | satP | b0010 | acetate/succinate:H(+) symporter |
| 3 | yaaW | (11356, 11356, 10743, 10643, 10743) | (0.05, 0.2, 0.2, 0.125, 0.05) | orange | 0.8 | 10999.5 | yaaW | b0011 | putative enzyme-specific chaperone YaaW |
| 4 | mbiA | (10830, 10830, 11215, 11315, 11215) | (0.05, 0.2, 0.2, 0.125, 0.05) | purple | 0.8 | 11072.5 | mbiA | b0012 | uncharacterized protein MbiA |
| 5 | yaaI | (11786, 11786, 11482, 11382, 11482) | (0.05, 0.2, 0.2, 0.125, 0.05) | orange | 0.8 | 11584.0 | yaaI | b0013 | DUF2541 domain-containing protein YaaI |