dash_bio_fornacontainer Examples and Reference

see FornaContainer in action.

FornaContainer

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

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Select the sequences to display below.

PDB_01019 
×
using Dash, DashBio

external_stylesheets = ["https://codepen.io/chriddyp/pen/bWLwgP.css"]

app = dash(external_stylesheets=external_stylesheets)

forna_sequences = Dict(
    "PDB_01019" => Dict(
        "sequence" => "AUGGGCCCGGGCCCAAUGGGCCCGGGCCCA",
        "structure" => ".((((((())))))).((((((()))))))"
    ),
    "PDB_00598" => Dict(
        "sequence" => "GGAGAUGACgucATCTcc",
        "structure" => "((((((((()))))))))"
    )
)

app.layout = html_div([
    dashbio_fornacontainer(
        id="my-default-forna"
    ),
    html_hr(),
    html_p("Select the sequences to display below."),
    dcc_dropdown(
        id="my-default-forna-sequence-display",
        options= [Dict("label" => name, "value" => name) for name in keys(forna_sequences)],
        multi=true,
        value=["PDB_01019"]
    )
])

callback!(app,
    Output("my-default-forna", "sequences"),
    [Input("my-default-forna-sequence-display", "value")]
) do value
    if value isa Nothing
        throw(PreventUpdate())
    end
    return [forna_sequences[selected_sequence] for selected_sequence in value]
end

run_server(app, "0.0.0.0", debug=true)

Customization

Height/Width

Change the size of the canvas component that holds the container.

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22nucleotide:22Cnucleotide:22nucleotide:23nucleotide:23Cnucleotide:23nucleotide:24nucleotide:24Gnucleotide:24nucleotide:25nucleotide:25Gnucleotide:25nucleotide:26nucleotide:26Gnucleotide:26nucleotide:27nucleotide:27Cnucleotide:27nucleotide:28nucleotide:28Cnucleotide:28nucleotide:29nucleotide:29Cnucleotide:29nucleotide:30nucleotide:30Anucleotide:30102030
using Dash, DashBio

app = dash()
sequences = [Dict(
    "sequence" => "AUGGGCCCGGGCCCAAUGGGCCCGGGCCCA",
    "structure" => ".((((((())))))).((((((()))))))"
)]

app.layout = dashbio_fornacontainer(
    sequences=sequences,
    height=300,
    width=500
)

run_server(app, "0.0.0.0", debug=true)

Disable Zoom And Pan

Specify whether zoom and pan interactions should be disabled.

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22nucleotide:22Cnucleotide:22nucleotide:23nucleotide:23Cnucleotide:23nucleotide:24nucleotide:24Gnucleotide:24nucleotide:25nucleotide:25Gnucleotide:25nucleotide:26nucleotide:26Gnucleotide:26nucleotide:27nucleotide:27Cnucleotide:27nucleotide:28nucleotide:28Cnucleotide:28nucleotide:29nucleotide:29Cnucleotide:29nucleotide:30nucleotide:30Anucleotide:30102030
using Dash, DashBio

app = dash()
sequences = [Dict(
    "sequence" => "AUGGGCCCGGGCCCAAUGGGCCCGGGCCCA",
    "structure" => ".((((((())))))).((((((()))))))"
)]

app.layout = dashbio_fornacontainer(
    sequences=sequences,
    allowPanningAndZooming=false
)

run_server(app, "0.0.0.0", debug=true)

Label Interval

Specify the interval at which the sequence positions should be labelled.

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Gnucleotide:9nucleotide:10nucleotide:10Gnucleotide:10nucleotide:11nucleotide:11Gnucleotide:11nucleotide:12nucleotide:12Cnucleotide:12nucleotide:13nucleotide:13Cnucleotide:13nucleotide:14nucleotide:14Cnucleotide:14nucleotide:15nucleotide:15Anucleotide:15nucleotide:16nucleotide:16Anucleotide:16nucleotide:17nucleotide:17Unucleotide:17nucleotide:18nucleotide:18Gnucleotide:18nucleotide:19nucleotide:19Gnucleotide:19nucleotide:20nucleotide:20Gnucleotide:20nucleotide:21nucleotide:21Cnucleotide:21nucleotide:22nucleotide:22Cnucleotide:22nucleotide:23nucleotide:23Cnucleotide:23nucleotide:24nucleotide:24Gnucleotide:24nucleotide:25nucleotide:25Gnucleotide:25nucleotide:26nucleotide:26Gnucleotide:26nucleotide:27nucleotide:27Cnucleotide:27nucleotide:28nucleotide:28Cnucleotide:28nucleotide:29nucleotide:29Cnucleotide:29nucleotide:30nucleotide:30Anucleotide:3036912151821242730
using Dash, DashBio

app = dash()

sequences = [Dict(
    "sequence" => "AUGGGCCCGGGCCCAAUGGGCCCGGGCCCA",
    "structure" => ".((((((())))))).((((((()))))))",
    "options" => Dict(
        "labelInterval" => 3
    )
)]

app.layout = dashbio_fornacontainer(
    sequences=sequences
)

run_server(app, "0.0.0.0", debug=true)

Fill Color For All Nodes

Change the color of all of the nucleotides in all sequences shown.

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22nucleotide:22Cnucleotide:22nucleotide:23nucleotide:23Cnucleotide:23nucleotide:24nucleotide:24Gnucleotide:24nucleotide:25nucleotide:25Gnucleotide:25nucleotide:26nucleotide:26Gnucleotide:26nucleotide:27nucleotide:27Cnucleotide:27nucleotide:28nucleotide:28Cnucleotide:28nucleotide:29nucleotide:29Cnucleotide:29nucleotide:30nucleotide:30Anucleotide:30102030
using Dash, DashBio

app = dash()
sequences = [Dict(
    "sequence" => "AUGGGCCCGGGCCCAAUGGGCCCGGGCCCA",
    "structure" => ".((((((())))))).((((((()))))))"
)]

app.layout = dashbio_fornacontainer(
    sequences=sequences,
    nodeFillColor="pink"
)

run_server(app, "0.0.0.0", debug=true)

Color Scheme

Change the parameter according to which the structure is colored.

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22nucleotide:22Cnucleotide:22nucleotide:23nucleotide:23Cnucleotide:23nucleotide:24nucleotide:24Gnucleotide:24nucleotide:25nucleotide:25Gnucleotide:25nucleotide:26nucleotide:26Gnucleotide:26nucleotide:27nucleotide:27Cnucleotide:27nucleotide:28nucleotide:28Cnucleotide:28nucleotide:29nucleotide:29Cnucleotide:29nucleotide:30nucleotide:30Anucleotide:30102030
using Dash, DashBio

app = dash()
sequences = [Dict(
    "sequence" => "AUGGGCCCGGGCCCAAUGGGCCCGGGCCCA",
    "structure" => ".((((((())))))).((((((()))))))"
)]

app.layout = dashbio_fornacontainer(
    sequences=sequences,
    colorScheme="positions"
)

run_server(app, "0.0.0.0", debug=true)

Custom Color Schemes For Different Sequences

Specify color schemes to be applied to all sequences in the container, or sequence-specific color schemes.

022fb054-c3b2-4c66-8e1f-d91aebeac72071fcbbb9-ad2e-4f7b-afa2-6474266c728f3f476427-d59c-4f97-a6da-39047882c92b022fb054-c3b2-4c66-8e1f-d91aebeac720bb3ef742-1ba9-435e-b4d4-37d5f12a22ce7d98bf23-0e40-4d9e-a3d3-76ee7b3bc887022fb054-c3b2-4c66-8e1f-d91aebeac720bb3ef742-1ba9-435e-b4d4-37d5f12a22cede58a764-f5fe-4dbc-8530-f5eaa5dfdf0e899fc90d-8b35-4a29-83b2-4798ea23aceabb3ef742-1ba9-435e-b4d4-37d5f12a22cede58a764-f5fe-4dbc-8530-f5eaa5dfdf0e71a0e6b4-6724-46cd-8a27-da39afda620f6572c9af-f912-4081-862d-750c2732e6d5de58a764-f5fe-4dbc-8530-f5eaa5dfdf0e71a0e6b4-6724-46cd-8a27-da39afda620fcca84b1d-08b5-451e-ac14-116274212b509363db68-82d1-4dd8-94da-b0d70fc7efc271a0e6b4-6724-46cd-8a27-da39afda620fcca84b1d-08b5-451e-ac14-116274212b5078faaf3d-c9f3-4aa1-89ac-edf3d28ac4c3a78e1f43-bc42-49b9-8387-9bec6777eb7acca84b1d-08b5-451e-ac14-116274212b5078faaf3d-c9f3-4aa1-89ac-edf3d28ac4c365a8748e-5e4b-47d4-853e-e58ecb2b06a12362e934-8c5e-47c5-a6f1-a0eb201ffcdb78faaf3d-c9f3-4aa1-89ac-edf3d28ac4c365a8748e-5e4b-47d4-853e-e58ecb2b06a12362e934-8c5e-47c5-a6f1-a0eb201ffcdb65a8748e-5e4b-47d4-853e-e58ecb2b06a1a78e1f43-bc42-49b9-8387-9bec6777eb7a78faaf3d-c9f3-4aa1-89ac-edf3d28ac4c32362e934-8c5e-47c5-a6f1-a0eb201ffcdba78e1f43-bc42-49b9-8387-9bec6777eb7a9363db68-82d1-4dd8-94da-b0d70fc7efc2cca84b1d-08b5-451e-ac14-116274212b50a78e1f43-bc42-49b9-8387-9bec6777eb7a9363db68-82d1-4dd8-94da-b0d70fc7efc26572c9af-f912-4081-862d-750c2732e6d571a0e6b4-6724-46cd-8a27-da39afda620f9363db68-82d1-4dd8-94da-b0d70fc7efc26572c9af-f912-4081-862d-750c2732e6d5899fc90d-8b35-4a29-83b2-4798ea23aceade58a764-f5fe-4dbc-8530-f5eaa5dfdf0e6572c9af-f912-4081-862d-750c2732e6d5899fc90d-8b35-4a29-83b2-4798ea23acea7d98bf23-0e40-4d9e-a3d3-76ee7b3bc887bb3ef742-1ba9-435e-b4d4-37d5f12a22ce899fc90d-8b35-4a29-83b2-4798ea23acea7d98bf23-0e40-4d9e-a3d3-76ee7b3bc88771fcbbb9-ad2e-4f7b-afa2-6474266c728f022fb054-c3b2-4c66-8e1f-d91aebeac7207d98bf23-0e40-4d9e-a3d3-76ee7b3bc88771fcbbb9-ad2e-4f7b-afa2-6474266c728f71fcbbb9-ad2e-4f7b-afa2-6474266c728f983f6ba7-c908-4ccd-a3a2-bb507736413902003295-c986-40e3-8cc0-9814fdd643e19678ed52-0170-43a0-be8f-5fdccc65ef78983f6ba7-c908-4ccd-a3a2-bb507736413902003295-c986-40e3-8cc0-9814fdd643e1beef498f-9443-4be5-a43b-60cae882820d2734d0b6-6dbc-43fe-8d0b-795030b41f9c02003295-c986-40e3-8cc0-9814fdd643e1beef498f-9443-4be5-a43b-60cae882820d3f3ead59-4bfe-40ec-8695-9c46149b6c9744935445-6ca3-44c2-b92a-99b43680868abeef498f-9443-4be5-a43b-60cae882820d3f3ead59-4bfe-40ec-8695-9c46149b6c97558f3237-e35d-47ac-8619-890e4cb6cf746fe11f44-02bd-4659-af81-883b187853223f3ead59-4bfe-40ec-8695-9c46149b6c97558f3237-e35d-47ac-8619-890e4cb6cf74a48cd1d9-1bb9-45ad-b797-7a5f35bb3d2fdc8b15b6-3428-48ed-88f2-79ff88b589fd558f3237-e35d-47ac-8619-890e4cb6cf74a48cd1d9-1bb9-45ad-b797-7a5f35bb3d2ff4ac666b-09db-4bcc-9b68-976a4bfdd6502967195d-5c84-41f4-b21a-0b3a47bc7e02a48cd1d9-1bb9-45ad-b797-7a5f35bb3d2ff4ac666b-09db-4bcc-9b68-976a4bfdd650935a74d0-b570-4091-be65-a50858a39a9fce6344e5-3a0c-429a-be5d-da503f4d4752f4ac666b-09db-4bcc-9b68-976a4bfdd650935a74d0-b570-4091-be65-a50858a39a9fce6344e5-3a0c-429a-be5d-da503f4d4752935a74d0-b570-4091-be65-a50858a39a9f2967195d-5c84-41f4-b21a-0b3a47bc7e02f4ac666b-09db-4bcc-9b68-976a4bfdd650ce6344e5-3a0c-429a-be5d-da503f4d47522967195d-5c84-41f4-b21a-0b3a47bc7e02dc8b15b6-3428-48ed-88f2-79ff88b589fda48cd1d9-1bb9-45ad-b797-7a5f35bb3d2f2967195d-5c84-41f4-b21a-0b3a47bc7e02dc8b15b6-3428-48ed-88f2-79ff88b589fd6fe11f44-02bd-4659-af81-883b18785322558f3237-e35d-47ac-8619-890e4cb6cf74dc8b15b6-3428-48ed-88f2-79ff88b589fd6fe11f44-02bd-4659-af81-883b1878532244935445-6ca3-44c2-b92a-99b43680868a3f3ead59-4bfe-40ec-8695-9c46149b6c976fe11f44-02bd-4659-af81-883b1878532244935445-6ca3-44c2-b92a-99b43680868a2734d0b6-6dbc-43fe-8d0b-795030b41f9cbeef498f-9443-4be5-a43b-60cae882820d44935445-6ca3-44c2-b92a-99b43680868a2734d0b6-6dbc-43fe-8d0b-795030b41f9c9678ed52-0170-43a0-be8f-5fdccc65ef7802003295-c986-40e3-8cc0-9814fdd643e12734d0b6-6dbc-43fe-8d0b-795030b41f9c9678ed52-0170-43a0-be8f-5fdccc65ef78a78e1f43-bc42-49b9-8387-9bec6777eb7ad5a9709c-67ed-4cd8-b234-450be24311b9558f3237-e35d-47ac-8619-890e4cb6cf74dad5c2ef-10ff-46ad-bd46-96d42dc70ca39678ed52-0170-43a0-be8f-5fdccc65ef78e9662362-3ef5-4a14-a22f-8e75d4be6d4f3afc53f0-1f27-4d4a-8a93-6c02454f1873ccd67a00-ce51-4894-929d-3325d7c47989a453eb79-9b92-4225-a74e-1749587fd599970a6f98-6420-4a12-b9be-fedab5a567d83afc53f0-1f27-4d4a-8a93-6c02454f1873a453eb79-9b92-4225-a74e-1749587fd599c33266c6-33ba-40e7-a6fb-c1a111d2575124435582-9bc5-4e4d-9707-972b46699850a453eb79-9b92-4225-a74e-1749587fd599c33266c6-33ba-40e7-a6fb-c1a111d2575102f280ff-3e94-4c85-a32b-74e7fdfe4ac9b15a43a2-af78-44f8-b032-cc0db3d3daa0c33266c6-33ba-40e7-a6fb-c1a111d2575102f280ff-3e94-4c85-a32b-74e7fdfe4ac95f415295-51da-4320-8ece-3a7371078df8cb4950b9-f509-4b9b-a114-2b893563c19b02f280ff-3e94-4c85-a32b-74e7fdfe4ac95f415295-51da-4320-8ece-3a7371078df8ac35944b-b287-4492-a402-87d0462d74616f16cfec-f325-4247-8861-c9f22119c6c75f415295-51da-4320-8ece-3a7371078df8ac35944b-b287-4492-a402-87d0462d7461339f8fa9-1379-47e4-a828-649ddde0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using Dash, DashBio

app = dash()
sequences = [
    Dict(
        "sequence" => "AUGGGCCCGGGCCCAAUGGGCCCGGGCCCA",
        "structure" => ".((((((())))))).((((((()))))))",
        "options" => Dict(
            "name" => "PDB_01019"
        )
    ),
    Dict(
        "sequence" => "GGAGAUGACgucATCTcc",
        "structure" => "((((((((()))))))))",
        "options" => Dict(
            "name" => "PDB_00598"
        )
    )
]

custom_colors = Dict(
    "domain" => [0, 100],
    "range" => ["rgb(175, 0, 255)", "orange"],
    "colorValues" => Dict(
        "" => Dict("1" => 10, "5" => 40),  # default; can be overridden by sequence-specific colorschemes below
        "PDB_01019" => Dict("10" => "rgb(120, 50, 200)", "13" => 50),
        "PDB_00598" => Dict(string(i) => string(i*5) for i in range(4, stop = length(sequences[1]["sequence"])))
    )
)

custom_colors["colorValues"]["PDB_00598"]["1"] = "red"
app.layout = dashbio_fornacontainer(
    sequences=sequences,
    colorScheme="custom",
    customColors=custom_colors
)
run_server(app, "0.0.0.0", debug=true)

FornaContainer Properties

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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.

height (Real; default 500): The height (in px) of the container in which the molecules will be displayed.

width (Real; default 300): The width (in px) of the container in which the molecules will be displayed.

sequences (Array of Dicts; optional): The molecules that will be displayed.

sequences is an Array of Dicts with keys:

  • options (Dict; optional): Additional options to be applied to the rendering of the RNA molecule.

    options is a Dict with keys:

    • 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.

    • avoidOthers (Bool; optional): Whether or not this molecule should "avoid" other molecules in the map.

    • 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.

  • 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.

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

colorScheme (a value equal to: 'sequence', 'structure', 'positions' or 'custom'; default 'sequence'): The color scheme that is used to color the nodes.

customColors (Dict; 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 is a Dict with keys:

  • 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.

  • 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.

allowPanningAndZooming (Bool; default true): 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.

hoverPattern (String; optional): Allow users to specify which information will be displayed after hover on the elements. To render node property place it into ${} construction. For example: 'Structure name is ${structName} - ${num}'. Acceptable node properties are "num", "radius", "rna", "nodeType", "structName", "size", "uid", "name".

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 (Bool; optional): Determines if the component is loading or not.

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

Example Data