Options

Selecting feature types and attributes

You can select which feature type to display. The default feature types are ["CDS", "repeat_region", "ncRNA", "rRNA", "tRNA"].

You can inspect the gff file to see what feature types and attributes are available. The genomenotebook.parse_gff function can conveniently be used for this purpose. It also accepts gzipped gff files.

import genomenotebook as gn
import os

data_path = gn.get_example_data_dir()
gff_path = os.path.join(data_path, "MG1655_U00096.gff3")
features = gn.parse_gff(gff_path)
features.head()

	seq_id	source	type	start	end	score	strand	phase	attributes	Parent	...	substrain	part	mobile_element_type	gene_biotype	gbkey	rpt_type	Name	left	right	middle
0	U00096.3	Genbank	region	1	4641652	.	+	.	ID=U00096.3:1..4641652;Dbxref=taxon:511145;Is_...	None	...	MG1655	None	None	None	Src	None	ANONYMOUS	1	4641652	2320826.5
1	U00096.3	Genbank	gene	190	255	.	+	.	ID=gene-b0001;Dbxref=ASAP:ABE-0000006,ECOCYC:E...	None	...	None	None	None	protein_coding	Gene	None	thrL	190	255	222.5
2	U00096.3	Genbank	CDS	190	255	.	+	0	ID=cds-AAC73112.1;Parent=gene-b0001;Dbxref=Uni...	gene-b0001	...	None	None	None	None	CDS	None	AAC73112.1	190	255	222.5
3	U00096.3	Genbank	gene	337	2799	.	+	.	ID=gene-b0002;Dbxref=ASAP:ABE-0000008,ECOCYC:E...	None	...	None	None	None	protein_coding	Gene	None	thrA	337	2799	1568.0
4	U00096.3	Genbank	CDS	337	2799	.	+	0	ID=cds-AAC73113.1;Parent=gene-b0002;Dbxref=Uni...	gene-b0002	...	None	None	None	None	CDS	None	AAC73113.1	337	2799	1568.0

5 rows × 39 columns

# Available feature types
set(features.type)

{'CDS',
 'exon',
 'gene',
 'mobile_genetic_element',
 'ncRNA',
 'origin_of_replication',
 'pseudogene',
 'rRNA',
 'recombination_feature',
 'region',
 'repeat_region',
 'sequence_feature',
 'tRNA'}

# Available attributes
features.columns

Index(['seq_id', 'source', 'type', 'start', 'end', 'score', 'strand', 'phase',
       'attributes', 'Parent', 'gene', 'transl_table', 'recombination_class',
       'orig_protein_id', 'product', 'protein_id', 'transl_except', 'strain',
       'gene_synonym', 'pseudo', 'exception', 'Note', 'orig_transcript_id',
       'Dbxref', 'genome', 'ID', 'locus_tag', 'Is_circular', 'mol_type',
       'substrain', 'part', 'mobile_element_type', 'gene_biotype', 'gbkey',
       'rpt_type', 'Name', 'left', 'right', 'middle'],
      dtype='object')

#Choosing the feature types, attributes and feature name to display
g=gn.GenomeBrowser(gff_path, 
                   feature_types = ["tRNA","rRNA"],
                   attributes = ["gene","locus_tag","strand","start","end"], #will be displayed when hovering 
                   init_pos=226000)
g.show()

Changing colors

Modifying features by type

The glyph shown for each feature type is defined through a Glyph object. A custom glyphs dictionnary can be passed to GenomeBrowser to customize the glyphs shown for different features.

glyphs=gn.get_default_glyphs()
glyphs['CDS']

Glyph object with attributes:
    glyph_type: arrow
    colors: ('purple', 'orange')
    height: 1
    alpha: 0.8
    show_name: True

glyphs['repeat_region']

Glyph object with attributes:
    glyph_type: box
    colors: ('grey',)
    height: 0.8
    alpha: 1
    show_name: False

Modifying the default glyphs

glyphs["CDS"].colors= ('blue','green')

g=gn.GenomeBrowser(gff_path, glyphs=glyphs, init_pos=224000, bounds=(220000,230000), search=False)
g.show()

Defining a new Glyph from scractch

glyphs["rRNA"]=gn.Glyph(glyph_type="box", 
                        colors="red", 
                        height=0.5, 
                        show_name=False)
                        
g=gn.GenomeBrowser(gff_path, glyphs=glyphs, init_pos=224000, bounds=(220000,230000), search=False)
g.show()

Modifying specific features

You can also access a DataFrame with the characteristics of each feature plotted on the genome browser. These can be modified as you wish to customize your plot.

g.patches.head()

	names	xs	ys	color	alpha	pos	gene	locus_tag	product
0	metQ	(220928, 220928, 220213, 220113, 220213)	(0.05, 0.2, 0.2, 0.125, 0.05)	green	0.8	220520.5	metQ	b0197	L-methionine/D-methionine ABC transporter memb...
1	metI	(221621, 221621, 221068, 220968, 221068)	(0.05, 0.2, 0.2, 0.125, 0.05)	green	0.8	221294.5	metI	b0198	L-methionine/D-methionine ABC transporter memb...
2	metN	(222645, 222645, 221714, 221614, 221714)	(0.05, 0.2, 0.2, 0.125, 0.05)	green	0.8	222129.5	metN	b0199	L-methionine/D-methionine ABC transporter ATP ...
3	gmhB	(222833, 222833, 223308, 223408, 223308)	(0.05, 0.2, 0.2, 0.125, 0.05)	blue	0.8	223120.5	gmhB	b0200	D-glycero-beta-D-manno-heptose-1%2C7-bisphosph...
4		(223771, 223771, 225312, 225312)	(0.0875, 0.1625, 0.1625, 0.0875)	red	0.8	224541.5	rrsH	b0201	16S ribosomal RNA

g=gn.GenomeBrowser(gff_path, init_pos=224000, bounds=(220000,230000), search=False)
g.patches.loc[g.patches.names=="metN","color"]="green"
g.show()

Customizing labels

Changing the attribute used as the feature name

You can chose which attribute of the GFF file should be displayed on top of the gene. The feature_name needs to belong to the list of attributes. The default list of attributes is [“locus_tag”,“gene”,“product”].

g=gn.GenomeBrowser(gff_path, 
                   attributes=["protein_id",'gene','product'], 
                   feature_name="protein_id",
                   bounds=(20000,30000),
                   search=False)
g.show()

Changing the name of specific features

You can also modify the names of specific features directly in the patches DataFrame

g.patches.head()

	names	xs	ys	color	alpha	pos	protein_id	gene	product
0	AAC73132.1	(20314, 20314, 19911, 19811, 19911)	(0.05, 0.2, 0.2, 0.125, 0.05)	orange	0.8	20062.5	AAC73132.1	insB-1	IS1 protein InsB
1	AAC73133.1	(20508, 20508, 20333, 20233, 20333)	(0.05, 0.2, 0.2, 0.125, 0.05)	orange	0.8	20370.5	AAC73133.1	insA-1	IS1 protein InsA
2	AAC73134.1	(21078, 21078, 20915, 20815, 20915)	(0.05, 0.2, 0.2, 0.125, 0.05)	orange	0.8	20946.5	AAC73134.1	rpsT	30S ribosomal subunit protein S20
3	AAC73135.1	(21181, 21181, 21299, 21399, 21299)	(0.05, 0.2, 0.2, 0.125, 0.05)	purple	0.8	21290.0	AAC73135.1	yaaY	DUF2575 domain-containing protein YaaY
4	AAC73136.1	(21407, 21407, 22248, 22348, 22248)	(0.05, 0.2, 0.2, 0.125, 0.05)	purple	0.8	21877.5	AAC73136.1	ribF	bifunctional riboflavin kinase/FMN adenylyltra...

g.patches.loc[g.patches.gene=="ribF","color"]="green"
g.patches.loc[g.patches.gene=="ribF","names"]="CUSTOM NAME"
g.show()

Changing label angle and size

g=gn.GenomeBrowser(gff_path,  
                   label_angle=0,
                   label_font_size="10pt",
                   height=80,
                   feature_height=0.4, #fraction of the annotation track occupied by the features
                   bounds=(20000,30000),
                   search=False)
g.show()

Adding information to be displayed when hovering

Any new column added to the patches DataFrame can be shown when hovering over features of the annotation track. The name of the column to display should also be provided as an attribute.

g=gn.GenomeBrowser(gff_path, 
                   init_pos=224000, 
                   bounds=(220000,230000), 
                   attributes=["gene","locus_tag","data"], 
                   search=False)
g.patches["data"]=np.random.randint(0,10,len(g.patches))
g.show()

Toolbar location

The location of the toolbar can be changed for each track independently. Placing it above or below can help see all the Bokeh tools available. Valid values are: * “above” * “below” * “left” * “right”

See the Bokeh documentation for more details.

import pandas as pd

data_path = gn.get_example_data_dir()
gff_path = os.path.join(data_path, "MG1655_U00096.gff3")

data=pd.DataFrame(dict(x=np.arange(0,50000,100),
                       y=np.sin(np.arange(0,50000,100))))

g=gn.GenomeBrowser(gff_path=gff_path, 
                bounds=(0,50000),
                toolbar_location="above",
                search=False)

track = g.add_track(height=200, 
                    toolbar_location="above")

track.bar(data=data, pos="x", y="y")
g.show()