dashbio_alignmentchart(;kwargs...)

An AlignmentChart component. The Alignment Chart (MSA) component is used to align multiple genomic or proteomic sequences from a FASTA or Clustal file. Among its extensive set of features, the multiple sequence alignment chart can display multiple subplots showing gap and conservation info, alongside industry standard colorscale support and consensus sequence. No matter what size your alignment is, Alignment Chart is able to display your genes or proteins snappily thanks to the underlying WebGL architecture powering the component. You can quickly scroll through your long sequence with a slider or a heatmap overview. Read more about the component here: https://github.com/plotly/react-alignment-viewer Keyword arguments:

• id (String; optional): The ID of this component, used to identify dash components

in callbacks. The ID needs to be unique across all of the components in an app.

• colorscale (String | Dict; optional): Colorscale in 'buried', 'cinema', 'clustal', 'clustal2', 'helix', 'hydrophobicity'

'lesk', 'mae', 'nucleotide', 'purine', 'strand', 'taylor', 'turn', 'zappo', or your own colorscale as a {'nucleotide': COLOR} dict. Note that this is NOT a standard plotly colorscale.

• conservationcolor (String; optional): Color of the conservation secondary barplot, in common name, hex, rgb or rgba format.
• conservationcolorscale (String | Array; optional): Colorscale of the conservation barplot, in Plotly colorscales (e.g. 'Viridis')

or as custom Plotly colorscale under a list format. Note that this conservationcolorscale argument does NOT follow the same format as the colorscale argument.

• conservationmethod (a value equal to: 'conservation', 'entropy'; optional): Whether to use most conserved ratio (MLE) 'conservation'

or normalized entropy 'entropy' to determine conservation, which is a value between 0 and 1 where 1 is most conserved.

• conservationopacity (Real | String; optional): Opacity of the conservation secondary barplot as a value between 0 and 1.
• correctgap (Bool; optional): Whether to normalize the conservation barchart

By multiplying it elementwise with the gap barchart, as to lower the conservation values across sequences regions with many gaps.

• data (String; optional): Input data, either in FASTA or Clustal format.
• eventDatum (String; optional): A Dash prop that returns data on clicking, hovering or resizing the viewer.
• extension (String; optional): Format type of the input data, either in FASTA or Clustal.
• gapcolor (String; optional): Color of the gap secondary barplot, in common name, hex, rgb or rgba format.
• gapcolorscale (String | Array; optional): Colorscale of the gap barplot, in Plotly colorscales (e.g. 'Viridis')

or as custom Plotly colorscale under a list format. Note that this conservationcolorscale argument does NOT follow the same format as the colorscale argument.

• gapopacity (Real | String; optional): Opacity of the gap secondary barplot as a value between 0 and 1.
• groupbars (Bool; optional): If both conservation and gap are enabled,

toggles whether to group bars or to stack them as separate subplots. No effect if not both gap and conservation are shown.

• height (Real | String; optional): Width of the Viewer.

Property takes precedence over tilesheight if both are set.

• numtiles (Real; optional): Sets how many tiles to display across horitontally. If enabled,

overrides tilewidth and sets the amount of tiles directly based off that value.

• opacity (Real | String; optional): Opacity of the main plot as a value between 0 and 1.
• overview (a value equal to: 'heatmap', 'slider', 'none'; optional): Toggles whether the overview should be a heatmap, a slider, or none.
• scrollskip (Real; optional): If overview is set to 'scroll', determines how many tiles to skip

with each slider movement. Has no effect if scroll is not enabled (such as with overview or none).

• showconsensus (Bool; optional): Displays toggling the consensus sequence, where each nucleotide in the

consensus sequence is the argmax of its distribution at a set nucleotide.

• showconservation (Bool; optional): Enables the display of conservation secondary barplot where the most conserved

nucleotides or amino acids get greater bars.

• showgap (Bool; optional): Enables the display of gap secondary barplot where the sequence regions

with the fewest gaps get the greatest bars.

• showid (Bool; optional): Toggles displaying sequence IDs at left of alignment.
• showlabel (Bool; optional): Toggles displaying sequence labels at left of alignment
• textcolor (String; optional): Color of the nucleotide labels, in common name, hex, rgb or rgba format.

If left blank, handled by the colorscale automatically.

• textsize (Real | String; optional): Size of the nucleotide labels, as a number.
• tickstart (Real | String; optional): Determines where to start annotating the first tile.

If let blank will be automatically determined by Plotly. Equivalent to Plotly's tick0 property. Does not function if overview mode 'slider' is applied. (Current bug)

• ticksteps (Real | String; optional): Determines at what interval to keep annotating the tiles.

If left blank will be automatially determined by Plotly. Equivalent to Plotly's dtick property. Does not function if overview mode 'slider' is applied. (Current bug)

• tileheight (Real; optional): Sets how many pixels each nucleotide/amino acid on the Alignment Chart

takes up vertically. If enabled, set height dynamically.

• tilewidth (Real; optional): Sets how many pixels each nucleotide/amino acid on the Alignment Chart

takes up horizontally. The total number of tiles (numtiles) seen horizontally is automatically determined by rounding the Viewer width divided by the tile width. the Viewwer width divided by the tile witdth.

• width (Real | String; optional): Width of the Viewer.

Property takes precedence over tileswidth and numtiles if either of them is set.

dashbio_fornacontainer(;kwargs...)

A FornaContainer component. FornaContainer is a force-directed graph that is used to visualize the secondary structure of biomolecules. It is based on the fornac library (https://github.com/ViennaRNA/fornac). Keyword arguments:

• id (String; optional): The ID of this component, used to identify dash components in

callbacks. The ID needs to be unique across all of the components in an app.

• allowPanningAndZooming (Bool; optional): Allow users to zoom in and pan the display. If this is enabled,

then pressing the 'c' key on the keyboard will center the view.

• colorScheme (a value equal to: 'sequence', 'structure', 'positions', 'custom'; optional): The color scheme that is used to color the nodes.
• customColors (optional): The custom colors used to color the nodes if the 'custom'

option is chosen for the colorScheme prop. For example, if the domain is [0, 20], the range is ['yellow', 'red'], and the dictionary specified in 'colorValues' that corresponds to a molecule is {'6': 10}, the sixth nucleotide in that molecule will have a color that is perfectly in between yellow and red (i.e., orange), since 10 is perfectly in between 0 and 20.. customColors has the following type: lists containing elements 'domain', 'range', 'colorValues'. Those elements have the following types:

• domain (Array of Reals; optional): The limits for the color scale. This is used with the range

specified in range to calculate the color of a given nucleotide, based on the number that it is assigned.

• range (Array of Strings; optional): The range of colors that will be used in conjunction with

the domain prop.

• colorValues (Dict with Strings as keys and values of type Dict with Strings as keys and values of type String | Real; optional): A dictionary which contains keys, each of which are either

an empty string ('') or the name of a molecule that has been defined in the name prop in the options for a sequence in the sequences property. The value corresponding to the key that is an empty string (if that key exists) is a "default" color scheme that will be applied first, and can be overridden by the color schemes defined for molecule-specific keys. The aforementioned color schemes each take the form of a dictionary in which the keys are the nucleotide positions and the values are either a) numbers to be normalized with respect to the scale defined in domain (so that their color will be calculated), or b) direct string representations of colors.

• height (Real; optional): The height (in px) of the container in which the molecules will

be displayed.

• nodeFillColor (String; optional): The fill color for all of the nodes. This will override any

color scheme defined in colorScheme.

• sequences (optional): The molecules that will be displayed.. sequences has the following type: Array of lists containing elements 'sequence', 'structure', 'options'.

Those elements have the following types:

• sequence (String; required): A string representing the RNA nucleotide sequence of

the RNA molecule.

• structure (String; required): A dot-bracket string

(https://software.broadinstitute.org/software/igv/RNAsecStructure) that specifies the secondary structure of the RNA molecule.

• options (optional): Additional options to be applied to the rendering of

the RNA molecule.. options has the following type: lists containing elements 'applyForce', 'circularizeExternal', 'labelInterval', 'name', 'avoidOthers'. Those elements have the following types:

• applyForce (Bool; optional): Indicate whether the force-directed layout will be

applied to the displayed molecule. Enabling this option allows users to change the layout of the molecule by selecting and dragging the individual nucleotide nodes. True by default.

• circularizeExternal (Bool; optional): This only makes sense in connection with the

applyForce argument. If it's true, the external loops will be arranged in a nice circle. If false, they will be allowed to flop around as the force layout dictates. True by default.

• labelInterval (Real; optional): Change how often nucleotide numbers are labelled

with their number. 10 by default.

• name (String; optional): The molecule name; this is used in custom color

scales.

• avoidOthers (Bool; optional): Whether or not this molecule should "avoid" other

molecules in the map.s

• width (Real; optional): The width (in px) of the container in which the molecules will

be displayed.

dashbio_ideogram(;kwargs...)

An Ideogram component. The Ideogram component is used to draw and animate genome-wide datasets for organisms such as human, mouse, and any other eukaryote. The Ideogram component can be used to compare homologous features between chromosomes, and depict haploid, diploid, aneuploid genomes. It can also display annotations on genomic data using histograms and overlays.

Reference: https://eweitz.github.io/ideogram/ Component's props: https://github.com/eweitz/ideogram/blob/master/api.md Keyword arguments:

• id (String; required): The ID used to identify this component in Dash callbacks and used to identify Ideogram

instances.

• ancestors (Dict; optional): A map associating ancestor labels to colors. Used to color

chromosomes from different ancestors in polyploid genomes.

• annotationHeight (Real; optional): Not used if annotationsLayout is set to "overlay".

The height of histogram bars or the size of annotations tracks symbols

• annotationTracks (Array of Dicts; optional): A list of objects with metadata for each track, e.g., id, display name, color, shape.
• annotations (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 has the following type: Array of lists containing elements 'name', 'chr', 'start', 'stop'. Those elements have the following types:

• name (String; optional)
• chr (String; optional)
• start (Real; optional)
• stop (Real; optional)s
• annotationsColor (String; optional): Color of annotations.
• 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

• annotationsLayout (a value equal to: 'tracks', 'histogram', 'overlay'; optional): 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).
• 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., "GCF000306695.2"), or GenBank accession (e.g., "GCA000005005.5")

• barWidth (Real; optional): 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 (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 has the following type: lists containing elements 'start', 'end', 'extent'. Those elements have the following types:

• start (String; optional)
• end (String; optional)
• extent (String; optional)
• chrHeight (Real; optional): The pixel height of the tallest chromosome in the ideogram
• chrMargin (Real; optional): The pixel space of margin between each chromosome.
• chrWidth (Real; optional): The pixel width of each chromosome.
• chromosomes (Array 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']

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

• filterable (Bool; optional): Whether annotations should be filterable or not.
• fullChromosomeLabels (Bool; optional): Whether to include abbreviation species name in chromosome label. Used for homology.
• histogramScaling (a value equal to: 'absolute', '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 (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 has the following type: lists containing elements 'chrOne', 'chrTwo'. Those elements have the following types:

• chrOne (optional): . chrOne has the following type: lists containing elements 'organism', 'start', 'stop'.

Those elements have the following types:

• organism (String; required)
• start (Array of Reals; optional)
• stop (Array of Reals; optional)
• chrTwo (optional): . chrTwo has the following type: lists containing elements 'organism', 'start', 'stop'.

Those elements have the following types:

• organism (String; required)
• start (Array of Reals; optional)
• stop (Array of Reals; optional)
• localOrganism (Dict; optional): Provide local JSON organism into this prop from a local user JSON file.

DataDir must not be initialized.

• organism (String | Real; optional): 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', '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 (Real; optional): The ploidy - number of chromosomes to depict for each chromosome set.
• ploidyDesc (Array of Dicts; optional): Description of ploidy in each chromosome set in terms of ancestry composition.
• rangeSet (Array of Dicts; optional): List of objects describing segments of recombination among chromosomes in a chromosome set.
• resolution (Real; 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 (Bool; optional): Whether chromosomes are rotatable on click.
• rotated (Bool; optional): Dash callback that returns true if rotated, and false if not.
• sex (a value equal to: 'male', 'female'; optional): Useful for omitting chromosome Y in female animals.

Currently only supported for organisms that use XY sex-determination.

• showAnnotTooltip (Bool; optional): Whether to show a tooltip upon mousing over an annotation.
• showBandLabels (Bool; optional): Whether to show cytogenetic band labels, e.g., 1q21.
• showChromosomeLabels (Bool; optional): Whether to show chromosome labels, e.g., 1, 2, 3, X, Y.
• showFullyBanded (Bool; optional): 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 (Bool; optional): Whether to show non-nuclear chromosomes,

e.g., for mitochondrial (MT) and chloroplast (CP) DNA.

• style (Dict; optional): The component's inline styles

dashbio_igv(;kwargs...)

An Igv component. The Igv component is an interactive genome visualization component developed by the Integrative Genomics Viewer (IGV) team. It uses an example integration of igv.js and React (https://www.npmjs.com/package/igv). Keyword arguments:

• id (String; optional): The ID of this component, used to identify dash components in callbacks.

The ID needs to be unique across all of the components in an app.

• className (String; optional): className of the component div.
• genome (String; optional): String identifier defining genome (e.g. "hg19"). See https://github.com/igvteam/igv.js/wiki/Reference-Genome for details and list of supported identifiers. Note: One (but only one) of either genome or reference properties must be set. If both are set, the genome property will be ignored.
• locus (String; optional): Initial genomic location(s). Either a string or an array of strings. If an array a viewport is created for each location.
• minimumBases (Real; optional): Minimum window size in base pairs when zooming in
• reference (Dict; optional): Object defining reference genome. see https://github.com/igvteam/igv.js/wiki/Reference-Genome Note: One (but only one) of either genome or reference properties must be set. If both are set, the genome property will be ignored.
• style (Dict; optional): Generic style overrides on the plot div
• tracks (Array; optional): Array of configuration objects defining tracks initially displayed when app launches. see https://github.com/igvteam/igv.js/wiki/Tracks-2.0

dashbio_molecule2dviewer(;kwargs...)

A Molecule2dViewer component. The Molecule2dViewer component is used to render structural formulae of molecules. Read more about the component here: https://github.com/Autodesk/molecule-2d-for-react Keyword arguments:

• id (String; optional): The ID used to identify this component in callbacks.
• height (Real; optional): The height of the SVG element.
• modelData (optional): Description of the molecule to display.. modelData has the following type: lists containing elements 'nodes', 'links'.

Those elements have the following types:

• nodes (optional): . nodes has the following type: Array of lists containing elements 'id', 'atom'.

Those elements have the following types:

• id (Real; optional)
• atom (String; optional)s
• links (optional): . links has the following type: Array of lists containing elements 'id', 'source', 'target', 'bond', 'strength', 'distance'.

Those elements have the following types:

• id (Real; optional)
• source (optional)
• target (optional)
• bond (Real; optional)
• strength (Real; optional)
• distance (Real; optional)s
• selectedAtomIds (Array of Reals; optional): The selected atom IDs.
• width (Real; optional): The width of the SVG element.

dashbio_molecule3dviewer(;kwargs...)

A Molecule3dViewer component. The Molecule3dViewer component is used to render schematic diagrams of biomolecules. It can display ribbon-structure diagrams, or render atoms in the molecule as sticks or spheres. Read more about the component here: https://github.com/Autodesk/molecule-3d-for-react Keyword arguments:

• id (String; optional): The ID used to identify this component in callbacks
• atomLabelsShown (Bool; optional): Property to either show or hide labels
• backgroundColor (String; optional): Property to change the background color of the molecule viewer
• backgroundOpacity (Real; optional): Property to change the background opacity - ranges from 0 to 1
• labels (Array of Dicts; optional): Labels corresponding to the atoms of the molecule.

Each label has a text field, a string containing the label content, and can have many other styling fields as described in https://3dmol.csb.pitt.edu/doc/types.html#LabelSpec

• modelData (optional): The data that will be used to display the molecule in 3D

The data will be in JSON format and should have two main dictionaries - atoms, bonds. modelData has the following type: lists containing elements 'atoms', 'bonds'. Those elements have the following types:

• atoms (Array; optional)
• bonds (Array; optional)
• orbital (optional): Add an isosurface from volumetric data provided in the cube_file. orbital has the following type: lists containing elements 'cubefile', 'isoval', 'opacity', 'positiveVolumetricColor', 'negativeVolumetricColor'.

Those elements have the following types:

• cube_file (String; optional): The filepath containing raw volumetric data for vertex coloring
• iso_val (Real; optional): The isovalue to draw the surface at
• opacity (Real; optional): Transparency of the surface, between 0 and 1
• positiveVolumetricColor (String; optional): Color for the positive value of the isosurface orbital
• negativeVolumetricColor (String; optional): Color for the negative value of the isosurface orbital
• selectedAtomIds (Array; optional): Property that stores a list of all selected atoms
• selectionType (a value equal to: 'atom', 'residue', 'chain'; optional): The selection type - may be atom, residue or chain
• shapes (Array of Dicts; optional): Add a predefined renderable shape objects to the molecule.

Valid shape types are Arrow, Sphere, and Cylinder.

• styles (optional): Property that can be used to change the representation of

the molecule. Options include sticks, cartoon and sphere. styles has the following type: Array of lists containing elements 'color', 'visualization_type'. Those elements have the following types:

• color (String; optional)
• visualization_type (a value equal to: 'cartoon', 'sphere', 'stick'; optional)s
• zoom (optional): Zoom the current view by a constant factor, with optional parameters

to modify the duration and motion of the zoom animation.. zoom has the following type: lists containing elements 'factor', 'animationDuration', 'fixedPath'. Those elements have the following types:

• factor (Real; optional): Magnification factor. Values greater than 1 will zoom,

in, less than one will zoom out. Default 2.

• animationDuration (Real; optional): An optional parameter that denotes the duration of a

zoom animation, in milliseconds.

• fixedPath (Bool; optional): If true, animation is constrained to requested motion,

overriding updates that happen during the animation.

• zoomTo (optional): Zoom to center of atom selection.. zoomTo has the following type: lists containing elements 'sel', 'animationDuration', 'fixedPath'.

Those elements have the following types:

• sel (optional): Selection specification specifying model and atom properties

to select. Default: all atoms in viewer.. sel has the following type: lists containing elements 'chain', 'res'. Those elements have the following types:

• chain (String; optional): Chain that the residue is located on.
• res (Real; optional): The index value used to identify the residue;

residues are numbered sequentially starting from 1.

• animationDuration (Real; optional): An optional parameter that denotes the duration of a zoom animation

, in milliseconds.

• fixedPath (Bool; optional): If true, animation is constrained to requested motion,

overriding updates that happen during the animation.

dashbio_needleplot(;kwargs...)

A NeedlePlot component. The Needle Plot component is used to visualize large datasets containing categorical or numerical data. The lines and markers in the plot correspond to bars in a histogram. Keyword arguments:

• id (String; optional): The ID of this component, used to identify dash components

in callbacks. The ID needs to be unique across all of the components in an app.

• domainStyle (optional): Options for the protein domain coloring. domainStyle has the following type: lists containing elements 'domainColor', 'displayMinorDomains'.

Those elements have the following types:

• domainColor (Array; optional)
• displayMinorDomains (Bool; optional)
• mutationData (optional): The data that are displayed on the plot. mutationData has the following type: lists containing elements 'x', 'y', 'mutationGroups', 'domains'.

Those elements have the following types:

• x (String | Array; optional)
• y (String | Array; optional)
• mutationGroups (Array of Strings; optional)
• domains (Array; optional)
• needleStyle (optional): Options for the needle marking single site mutations. needleStyle has the following type: lists containing elements 'stemColor', 'stemThickness', 'stemConstHeight', 'headSize', 'headColor', 'headSymbol'.

Those elements have the following types:

• stemColor (String; optional)
• stemThickness (Real; optional)
• stemConstHeight (Bool; optional)
• headSize (Real; optional)
• headColor (Array | String; optional)
• headSymbol (Array | String; optional)
• rangeSlider (Bool; optional): If true, enables a rangeslider for the x-axis.
• xlabel (String; optional): Title of the x-axis.
• ylabel (String; optional): Title of the y-axis.

dashbio_nglmoleculeviewer(;kwargs...)

A NglMoleculeViewer component. The NglMoleculeViewer is used to render schematic diagrams of biomolecules in ribbon-structure representations. Read more about the component here: https://github.com/IvoLeist/dash_ngl Read more about the used WebGL protein viewer here: https://github.com/arose/ngl Keyword arguments:

• id (String; optional): The ID of this component, used to identify dash components in callbacks.

The ID needs to be unique across all of the components in an app.

• data (optional): The data (in JSON format) that will be used to display the molecule

filename: name of the used pdb/cif file ext: file extensions (pdb or cif) selectedValue: pdbString chain: ALL if the whole molecule shoud be displayed, e.g. A for showing only chain A aaRange: ALL if the whole molecule should be displayed, e.g. 1:50 for showing only 50 atoms color: chain color chosen.atoms: string of the chosen Atoms, e.g. 50,100,150 –> chosen eatoms changed to colored 'ball' chosen.residues: string of the chosen residues, e.g. 50,100,150 –> C alpha of chosen residue changed to colored 'ball' config.input: content of the pdb file config.type: format of config.input uploaded: bool if file from local storage (false) or uploaded by user (true) resetView: bool if the selection did not change but the view should be resettet (true). data has the following type: Array of lists containing elements 'filename', 'ext', 'selectedValue', 'chain', 'aaRange', 'color', 'chosen', 'config', 'uploaded', 'resetView'. Those elements have the following types:

• filename (String; required)
• ext (String; optional)
• selectedValue (String; required)
• chain (String; required)
• aaRange (String; required)
• color (String; required)
• chosen (optional): . chosen has the following type: lists containing elements 'residues', 'atoms'.

Those elements have the following types:

• residues (String; required)
• atoms (String; required)
• config (optional): . config has the following type: lists containing elements 'input', 'type'.

Those elements have the following types:

• input (String; required)
• type (String; required)
• uploaded (Bool; required)
• resetView (Bool; required)s
• downloadImage (Bool; optional): flag if download image was selected
• height (String | Real; optional): The height (in px or as a number) of the container

in which the molecules will be displayed.

• imageParameters (optional): Parameters (in JSON format) for exporting the image. imageParameters has the following type: lists containing elements 'antialias', 'transparent', 'trim', 'defaultFilename'.

Those elements have the following types:

• antialias (Bool; optional)
• transparent (Bool; optional)
• trim (Bool; optional)
• defaultFilename (String; optional)
• molStyles (optional): The data (in JSON format) that will be used to style the displayed molecule

representations: one or multiple selected molecule representation

• Possible molecule styles: 'backbone,'ball+stick','cartoon', 'hyperball','licorice','line', 'ribbon',''rope','spacefill','surface','trace','tube'
• Possible additional representations: 'axes','axes+box','helixorient','unitcell'

chosenAtomsColor: color of the 'ball+stick' representation of the chosen atoms chosenAtomsRadius: radius of the 'ball+stick' representation of the chosen atoms molSpacingXaxis: distance on the xAxis between each molecule. molStyles has the following type: lists containing elements 'representations', 'chosenAtomsColor', 'chosenAtomsRadius', 'molSpacingXaxis', 'sideByside'. Those elements have the following types:

• representations (Array of Strings; optional)
• chosenAtomsColor (String; required)
• chosenAtomsRadius (Real; required)
• molSpacingXaxis (Real; required)
• sideByside (Bool; required)
• pdbString (String; optional): Variable which defines how many molecules should be shown and/or which chain

The following format needs to be used: pdbID1.chain:start-end@atom1,atom2_pdbID2.chain:start-end . indicates that only one chain should be shown : indicates that a specific amino acids range should be shown (e.g. 1-50) @ indicates that chosen atoms should be highlighted (e.g. @50,100,150) _ indicates that more than one protein should be shown

• stageParameters (optional): Parameters (in JSON format) for the stage object of ngl.

Currently implemented are render quality, background color and camera type quality: auto, low, medium, high (default: auto) backgroundColor: white / black (default: white) cameraType: perspective / orthographic (default: perspective). stageParameters has the following type: lists containing elements 'quality', 'backgroundColor', 'cameraType'. Those elements have the following types:

• quality (String; optional)
• backgroundColor (String; optional)
• cameraType (String; optional)
• width (String | Real; optional): The width (in px or as a number) of the container

in which the molecules will be displayed.

dashbio_oncoprint(;kwargs...)

An OncoPrint component. The OncoPrint component is used to view multiple genetic alteration events through an interactive and zoomable heatmap. It is a React/Dash port of the popular oncoPrint() function from the BioConductor R package. Under the hood, the rendering is done using Plotly.js built upon D3. Plotly's interactivity allows the user to bind clicks and hovers to genetic events, allowing the user to create complex bioinformatic apps or workflows that rely on crossfiltering. Read more about the component here: https://github.com/plotly/react-oncoprint Keyword arguments:

• id (String; optional): The ID of this component, used to identify dash components

in callbacks. The ID needs to be unique to the component.

• backgroundcolor (String; optional): Default color for the tracks, in common name, hex, rgb or rgba format.

If left blank, will default to a light grey rgb(190, 190, 190).

• colorscale (Bool | Dict; optional): If not null, will override the default OncoPrint colorscale.

Default OncoPrint colorscale same as CBioPortal implementation. Make your own colrscale as a {'mutation': COLOR} dict. Supported mutation keys are ['MISSENSE, 'INFRAME', 'FUSION', 'AMP', 'GAIN', 'HETLOSS', 'HMODEL', 'UP', 'DOWN'] Note that this is NOT a standard plotly colorscale.

• data (Array; optional): Input data, in CBioPortal format where each list entry is a dict

consisting of 'sample', 'gene', 'alteration', and 'type'

• eventDatum (Dict; optional): A Dash prop that returns data on clicking, hovering or resizing the viewer.
• height (Real | String; optional): Height of the OncoPrint.

Will disable auto-resizing of plots if set.

• padding (Real; optional): Adjusts the padding (as a proportion of whitespace) between two tracks.

Value is a ratio between 0 and 1. Defaults to 0.05 (i.e., 5 percent). If set to 0, plot will look like a heatmap.

• range (Array; optional): .Toogles whether or not to show a legend on the right side of the plot,

with mutation information.

• showlegend (Bool; optional): .Toogles whether or not to show a legend on the right side of the plot,

with mutation information.

• showoverview (Bool; optional): .Toogles whether or not to show a heatmap overview of the tracks.
• width (Real | String; optional): Width of the OncoPrint.

Will disable auto-resizing of plots if set.

dashbio_sequenceviewer(;kwargs...)

A SequenceViewer component. The sequence viewer component is used to display sequences that represent proteins, strands of genomic information, and more. It can apply a coverage to the sequence supplied (with clickable coverage sections that can display specific information, and an optional legend to describe the color codes used), search through the sequence for specific regex, capture mouse selection events of subparts of the sequence, display a count of the number of nucleotides or amino acids in the sequence, Read more about the component here: https://github.com/FlyBase/react-sequence-viewer Keyword arguments:

• id (String; optional): The ID used to identify this component in Dash callbacks.
• badge (Bool; optional): The option of whether or not to display a badge showing the

amino acid count at the top of the component beside the title.

• charsPerLine (Real; optional): The number of amino acids that will display per line.
• coverage (optional): A coverage of the entire sequence; each section of the sequence

can have its own text color, background color, tooltip (on hover), and an optional underscore. The props start and end represent the beginning and terminating indices of the section in question. Cannot be used at the same time as selection.. coverage has the following type: Array of lists containing elements 'start', 'end', 'color', 'bgcolor', 'tooltip', 'underscore', 'onclick'. Those elements have the following types:

• start (Real; optional)
• end (Real; optional)
• color (String; optional)
• bgcolor (String; optional)
• tooltip (String; optional)
• underscore (Bool; optional)
• onclick (optional)s
• coverageClicked (Real; optional): Contains the index of the section that was clicked last in

the coverage list supplied.

• legend (optional): A legend corresponding to the color codes above (optionally displayed).. legend has the following type: Array of lists containing elements 'name', 'color', 'underscore'.

Those elements have the following types:

• name (String; optional)
• color (String; optional)
• underscore (Bool; optional)s
• mouseSelection (optional): Contains information about the subsequence selected

by the mouse. Start and end refer to the initial and final indices, respectively, of the subsequence, and "selection" contains the string that is selected.. mouseSelection has the following type: lists containing elements 'start', 'end', 'selection'. Those elements have the following types:

• start (Real; optional)
• end (Real; optional)
• selection (String; optional)
• search (Bool; optional): The option of whether or not to include a search bar in

the header. This supports regex.

• selection (optional): A highlighted section of the sequence; the color of the highlight

can also be defined. Takes a list of format [min, max, color] where min is a number that represents the starting index of the selection, max is a number that represents the stopping index of the selection, and color is a string that defines the highlight color. Cannot be used at the same time as coverage.

• sequence (String; optional): The amino acid sequence that will be displayed.
• sequenceMaxHeight (String; optional): The maximum height of the sequence.
• showLineNumbers (Bool; optional): The option of whether or not to display line numbers.
• subpartSelected (optional): A list of the subparts selected using the

"search" function or the "selection" property.. subpartSelected has the following type: Array of lists containing elements 'start', 'end', 'sequence'. Those elements have the following types:

• start (Real; optional)
• end (Real; optional)
• sequence (String; optional)s
• title (String; optional): A string that displays at the top of the component.
• toolbar (Bool; optional): The option of whether or not to display a toolbar at the top

that allows the user to choose the number of letters per line.

• wrapAminoAcids (Bool; optional): The option of whether or not to display the list of amino acids

as broken up into separate lines of a fixed length set by charsPerLine.

dashbio_speck(;kwargs...)

A Speck component. The Speck component is a WebGL-based 3D molecule renderer. Read more about the component here: https://github.com/wwwtyro/speck Keyword arguments:

• id (String; optional): The ID used to identify this component in Dash callbacks.
• data (optional): The xyz file data; a list of atoms such that each atom

has a dictionary defining the x, y, and z coordinates along with the atom's symbol.. data has the following type: Array of lists containing elements 'symbol', 'x', 'y', 'z'. Those elements have the following types:

• symbol (String; optional)
• x (Real; optional)
• y (Real; optional)
• z (Real; optional)s
• presetView (a value equal to: 'default', 'stickball', 'toon', 'licorice'; optional): One of several pre-loaded views: default, stick-ball, toon,

and licorice

• scrollZoom (Bool; optional): The option of whether or not to allow scrolling to control

the zoom.

• view (optional): An object that determines and controls various parameters

related to how the molecule is displayed.. view has the following type: lists containing elements 'aspect', 'zoom', 'translation', 'atomScale', 'relativeAtomScale', 'bondScale', 'rotation', 'ao', 'aoRes', 'brightness', 'outline', 'spf', 'bonds', 'bondThreshold', 'bondShade', 'atomShade', 'resolution', 'dofStrength', 'dofPosition', 'fxaa'. Those elements have the following types:

• aspect (Real; optional)
• zoom (Real; optional)
• translation (optional): . translation has the following type: lists containing elements 'x', 'y'.

Those elements have the following types:

• x (Real; optional)
• y (Real; optional)
• atomScale (Real; optional)
• relativeAtomScale (Real; optional)
• bondScale (Real; optional)
• rotation (optional): . rotation has the following type: lists containing elements .

Those elements have the following types:

• ao (Real; optional)
• aoRes (Real; optional)
• brightness (Real; optional)
• outline (Real; optional)
• spf (Real; optional)
• bonds (Bool; optional)
• bondThreshold (Real; optional)
• bondShade (Real; optional)
• atomShade (Real; optional)
• resolution (Real; optional)
• dofStrength (Real; optional)
• dofPosition (Real; optional)
• fxaa (Real; optional)