dash_bio.Ideogram Examples and Reference

see Ideogram in action.

Ideogram

An example of a default Ideogram component without any extra properties.

Select which chromosomes to display on the ideogram below: 
from dash import Dash, html, dcc, Input, Output, callback
import dash_bio as dashbio

app = Dash()

app.layout = html.Div([
    'Select which chromosomes to display on the ideogram below:',
    dcc.Dropdown(
        id='my-default-displayed-chromosomes',
        options=[{'label': str(i), 'value': str(i)} for i in range(1, 23)],
        multi=True,
        value=[str(i) for i in range(1, 23)]
    ),
    dashbio.Ideogram(
        id='my-default-dashbio-ideogram'
    ),
    html.Div(id='my-default-ideogram-rotated')
])

@callback(
    Output('my-default-dashbio-ideogram', 'chromosomes'),
    Input('my-default-displayed-chromosomes', 'value')
)
def update_ideogram(value):
    return value

@callback(
    Output('my-default-ideogram-rotated', 'children'),
    Input('my-default-dashbio-ideogram', 'rotated')
)
def update_ideogram_rotated(rot):
    return 'You have {} selected a chromosome.'.format(
        '' if rot else 'not')

if __name__ == '__main__':
    app.run(debug=True)

Customization

Height/Width

Change the size of the chromosomes in your ideogram.

import dash_bio as dashbio

dashbio.Ideogram(
    id='ideogram-size',
    chrHeight=800,
    chrWidth=100
)

Annotations

Display annotations that are loaded from a JSON file.

import dash_bio as dashbio

dashbio.Ideogram(
    id='ideogram-annotations',
    chromosomes=['X', 'Y'],
    annotationsPath='https://eweitz.github.io/ideogram/data/annotations/SRR562646.json'
)

Rotatability

Disable rotation of the chromosome upon clicking on it.

import dash_bio as dashbio

dashbio.Ideogram(
    id='ideogram-rotate',
    rotatable=False
)

Orientation

Display chromosomes horizontally or vertically.

import dash_bio as dashbio

dashbio.Ideogram(
    id='ideogram-orientation',
    orientation='horizontal'
)

Brush

Highlight a region of the chromosome by adding a brush.

import dash_bio as dashbio

dashbio.Ideogram(
    id='ideogram-brush',
    chromosomes=['X'],
    orientation='horizontal',
    brush='chrX:1-10000000'
)

Ideogram Properties

Access this documentation in your Python terminal with:
```python

help(dash_bio.Ideogram)
```

Our recommended IDE for writing Dash apps is Dash Enterprise’s
Data Science Workspaces,
which has typeahead support for Dash Component Properties.
Find out if your company is using
Dash Enterprise.

id (string; required):
The ID used to identify this component in Dash callbacks and used to
identify Ideogram instances.

style (dict; optional):
The component’s inline styles.

className (string; optional):
The CSS class of the component wrapper.

accessToken (string; optional):
OAuth 2.0 access token. Enables authentication and authorization. This
can be useful for controlling access to private annotation data.

ancestors (dict; optional):
A map associating ancestor labels to colors. Used to color chromosomes
from different ancestors in polyploid genomes.

annotations (list of dicts; optional):
A list of annotation objects. Annotation objects can also have a name,
color, shape, and track index. At the moment there is more keys
specified and the docs need updating.

annotations is a list of dicts with keys:

  • chr (string; optional)

  • color (string; optional)

  • index (number; optional)

  • name (string; optional)

  • shape (string; optional)

  • start (number; optional)

  • stop (number; optional)

annotationHeight (number; optional):
Not used if annotationsLayout is set to “overlay”. The height of
histogram bars or the size of annotations tracks symbols.

annotationsColor (string; default '#F00'):
The color of each annotation.

annotationsLayout (a value equal to: ‘tracks’, ‘histogram’ or ‘overlay’; default 'tracks'):
Layout of ideogram annotations. One of “tracks”, “histogram”, or
“overlay”. “tracks”: display annotations in tracks beside each
chromosome. “histogram”: display annotations in a histogram. Clusters
annotations by location. Each cluster/bin is shown as a bar, the
height of which represents the number of annotations on genomic range.
“overlay”: display annotations directly over chromosomes.

annotationsPath (string; optional):
An absolute or relative URL directing to a JSON file containing
annotation objects (JSON).

annotationsData (string; optional):
Use this prop in a dash callback to return annotationData when
hovered. It is read-only, i.e., it cannot be used with
dash.dependencies.Output but only with dash.dependencies.Input.

annotationTracks (list of dicts; optional):
A list of objects with metadata for each track, e.g., id, display
name, color, shape.

assembly (string; optional):
Default: latest RefSeq assembly for specified organism. The genome
assembly to display. Takes assembly name (e.g., “GRCh37”), RefSeq
accession (e.g., “GCF_000306695.2”), or GenBank accession (e.g.,
“GCA_000005005.5”).

barWidth (number; default 3):
Pixel width of histogram bars. Only used if annotationsLayout is set
to “histogram”.

brush (string; optional):
Genomic coordinate range (e.g., “chr1:104325484-119977655”) for a
brush on a chromosome. Useful when ideogram consists of one chromosome
and you want to be able to focus on a region within that chromosome,
and create an interactive sliding window to other regions.

brushData (dict; optional):
A dash callback that is activated when the ‘brush’ prop is used. It
will return an dictionary like so: {‘start’: <value>, ‘end’: <value>,
‘extent’: <value>} where start is the left most edge, end is right
most edge, and extent is the total width of the brush. It is
read-only, i.e., it cannot be used with dash.dependencies.Output but
only with dash.dependencies.Input.

brushData is a dict with keys:

  • end (string; optional)

  • extent (string; optional)

  • start (string; optional)

chrHeight (number; default 400):
The pixel height of the tallest chromosome in the ideogram.

chrMargin (number; default 10):
The pixel space of margin between each chromosome.

chrWidth (number; default 10):
The pixel width of each chromosome.

chromosomes (list of strings | dict; optional):
A list of the names of chromosomes to display. Useful for depicting a
subset of the chromosomes in the genome, e.g., a single chromosome. If
Homology (between two different species): Ex: chromosomes={
‘human’: [‘1’], ‘mouse’: [‘4’] } General case to specify
specific chromosomes: Ex: chromosomes=[‘1’, ‘2’].

chromosomeScale (a value equal to: ‘absolute’ or ‘relative’; optional):
Used when comparing multiple genomes. “absolute”: chromosomes will be
scaled by base pairs in each genome. “relative”: first chromosome in
each genome is of equal length; subsequent chromosomes will be scaled
relative to the first chromosome.

container (string; optional):
CSS styling and the id of the container holding the Ideogram in
react-ideogram.js, this is where all the d3 magic happens.

dataDir (string; default 'https://unpkg.com/ideogram/dist/data/bands/native/'):
Absolute or relative URL of the directory containing data needed to
draw banded chromosomes. You will need to set up your own database to
grab data from a custom database.

demarcateCollinearChromosomes (boolean; optional):
Whether to demarcate colllinear chromosomes. Puts a dark border around
the perimeter of each track-chromosomes block in track sets for
chromosomes arranged in collinear geometry.

geometry (a value equal to: ‘collinear’ or ‘parallel’; optional):
The arrangement of chromosomes. “collinear”: arrange all chromosomes
in one line. “parallel”: arrange chromosomes to be parallel to one
another.

heatmaps (list of dicts; optional):
Array of heatmap objects. Each heatmap object has a key string and a
thresholds array. The key property specifies the annotations key value
to depict in the heatmap. The thresholds property specifies a list of
two-element “threshold” lists, where the first element is the
threshold value and the second is the threshold color. The threshold
values are a list of ranges to use in coloring the heatmap. Threshold
values are specified in ascending order.

heatmaps is a list of dicts with keys:

  • key (string; optional)

  • thresholds (list of lists; optional)

histogramScaling (a value equal to: ‘absolute’ or ‘relative’; optional):
Scaling of histogram bars height Only used if annotationsLayout is set
to “histogram”. One of “absolute” or “relative”. “absolute”: sets bar
height relative to tallest bar in all chromosomes. “relative”: sets
bar height relative to tallest bar in each chromosome.

homology (dict; optional):
Used to compare two chromosomes. The keys “chrOne” and “chrTwo”
represent one chromosome each. Organism is the taxID or name. Start
is an array, containing start one and start two, in this order. Stop
is an array, containing stop one, and stop two, in this order. Ex:
homology={ “chrOne”: { organism”: “9606”, “start”: [50000, 155701383],
“stop”: [900000, 156030895] }, “chrTwo”: { organism”: “10090”,
“start”: [10001, 50000000], “stop”: [2781479, 57217415] } }.

homology is a dict with keys:

  • chrOne (dict; optional)

    chrOne is a dict with keys:

    • organism (string; required)

    • start (list of numbers; optional)

    • stop (list of numbers; optional)

  • chrTwo (dict; optional)

    chrTwo is a dict with keys:

    • organism (string; required)

    • start (list of numbers; optional)

    • stop (list of numbers; optional)

filterable (boolean; optional):
Whether annotations should be filterable or not.

fullChromosomeLabels (boolean; optional):
Whether to include abbreviation species name in chromosome label. Used
for homology.

legend (list of dicts; optional)

legend is a list of dicts with keys:

  • name (string; optional)

  • rows (list of dicts; optional)

    rows is a list of dicts with keys:

    • color (string; optional)

    • name (string; optional)

    • shape (a value equal to: ‘circle’, ‘triangle’ or ‘rectangle’; optional)

organism (string | number; default 'human'):
Organism(s) to show chromosomes for. Supply organism’s name as a
string (e.g., “human”) or organism’s NCBI Taxonomy ID (taxid, e.g.,
9606) to display chromosomes from a single organism, or an array of
organisms’ names or taxids to display chromosomes from multiple
species.

orientation (a value equal to: ‘vertical’ or ‘horizontal’; optional):
The orientation of chromosomes on the page.

perspective (a value equal to: ‘comparative’; optional):
Use perspective: ‘comparative’ to enable annotations between two
chromosomes, either within the same organism or different organisms.
Used for homology.

ploidy (number; default 1):
The ploidy - number of chromosomes to depict for each chromosome set.

ploidyDesc (list of dicts; optional):
Description of ploidy in each chromosome set in terms of ancestry
composition.

rangeSet (list of dicts; optional):
List of objects describing segments of recombination among chromosomes
in a chromosome set.

resolution (number; optional):
The resolution of cytogenetic bands to show for each chromosome. The
quantity refers to an approximate value in bands per haploid set
(bphs). One of 450, 550, or 850.

rotatable (boolean; default True):
Whether chromosomes are rotatable on click.

rotated (boolean; optional):
Dash callback that returns True if rotated, and False if not.

rows (number; default 1):
Number of rows to arrange chromosomes into. Useful for putting
ideogram into a small container, or when dealing with genomes that
have many chromosomes.

sex (a value equal to: ‘male’ or ‘female’; optional):
The biological sex of the organism. Useful for omitting chromosome Y
in female animals. Currently only supported for organisms that use XY
sex-determination.

showAnnotTooltip (boolean; default True):
Whether to show a tooltip upon mousing over an annotation.

showBandLabels (boolean; default False):
Whether to show cytogenetic band labels, e.g., 1q21.

showChromosomeLabels (boolean; default True):
Whether to show chromosome labels, e.g., 1, 2, 3, X, Y.

showFullyBanded (boolean; default True):
Whether to show fully banded chromosomes for genomes that have
sufficient data. Useful for showing simpler chromosomes of
cytogenetically well-characterized organisms, e.g., human, beside
chromosomes of less studied organisms, e.g., chimpanzee.

showNonNuclearChromosomes (boolean; default False):
Whether to show non-nuclear chromosomes, e.g., for mitochondrial (MT)
and chloroplast (CP) DNA.

loading_state (dict; optional):
Object that holds the loading state object coming from dash-renderer.

loading_state is a dict with keys:

  • component_name (string; optional):
    Holds the name of the component that is loading.

  • is_loading (boolean; optional):
    Determines if the component is loading or not.

  • prop_name (string; optional):
    Holds which property is loading.

Example Data