import gradio as gr from app import demo as app import os _docs = {'IGV': {'description': 'IGV Browser component.', 'members': {'__init__': {'value': {'type': 'Any', 'default': 'None', 'description': None}, 'label': {'type': 'str | None', 'default': 'None', 'description': None}, 'info': {'type': 'str | None', 'default': 'None', 'description': None}, 'show_label': {'type': 'bool | None', 'default': 'None', 'description': None}, 'container': {'type': 'bool', 'default': 'True', 'description': None}, 'scale': {'type': 'int | None', 'default': 'None', 'description': None}, 'min_width': {'type': 'int | None', 'default': 'None', 'description': None}, 'interactive': {'type': 'bool | None', 'default': 'None', 'description': None}, 'visible': {'type': 'bool', 'default': 'True', 'description': None}, 'elem_id': {'type': 'str | None', 'default': 'None', 'description': None}, 'elem_classes': {'type': 'list[str] | str | None', 'default': 'None', 'description': None}, 'render': {'type': 'bool', 'default': 'True', 'description': None}, 'key': {'type': 'int | str | None', 'default': 'None', 'description': None}, 'load_fn': {'type': 'Callable | None', 'default': 'None', 'description': None}, 'every': {'type': 'Timer | float | None', 'default': 'None', 'description': None}, 'inputs': {'type': 'Component | Sequence[Component] | set[Component] | None', 'default': 'None', 'description': None}}, 'postprocess': {'value': {'type': 'IGVContext', 'description': None}}, 'preprocess': {'return': {'type': 'IGVContext', 'description': None}, 'value': None}}, 'events': {'trackremoved': {'type': None, 'default': None, 'description': 'Triggered when a track is removed from the IGV Browser.'}, 'trackdrag': {'type': None, 'default': None, 'description': 'Triggered when a track is dragged in the IGV Browser.'}, 'trackdragend': {'type': None, 'default': None, 'description': 'Triggered when a track is finished being dragged in the IGV Browser.'}, 'locuschange': {'type': None, 'default': None, 'description': 'Triggered when the locus is changed in the IGV Browser.'}, 'trackclick': {'type': None, 'default': None, 'description': 'Triggered when a track is clicked in the IGV Browser.'}, 'trackorderchanged': {'type': None, 'default': None, 'description': 'Triggered when the order of tracks is changed in the IGV Browser.'}}}, '__meta__': {'additional_interfaces': {'IGVContext': {'source': 'class IGVContext(GradioModel):\n genome: str | ReferenceGenome = Field(default="hg38")\n locus: str = Field(default="")\n loadAlignmentTracks: list[AlignmentTrackLoad] = Field(\n default_factory=list\n )\n loadVariantTracks: list[VariantTrackLoad] = Field(\n default_factory=list\n )\n loadAnnotationTracks: list[AnnotationTrackLoad] = Field(\n default_factory=list\n )\n removeTracks: list[str] = Field(default_factory=list)\n\n def update_genome(self, genome: str | ReferenceGenome):\n self.genome = genome\n return self\n\n def update_locus(self, locus: str):\n self.locus = locus\n return self\n\n def add_track(self, track_load: TrackLoad):\n if isinstance(track_load, AlignmentTrackLoad):\n self.loadAlignmentTracks.append(track_load)\n elif isinstance(track_load, VariantTrackLoad):\n self.loadVariantTracks.append(track_load)\n elif isinstance(track_load, AnnotationTrackLoad):\n self.loadAnnotationTracks.append(track_load)\n else:\n raise ValueError(\n "TrackLoad type not recognized."\n )\n\n return self\n\n def remove_track(self, track: str):\n self.removeTracks.append(track)\n return self', 'refs': ['ReferenceGenome', 'AlignmentTrackLoad', 'VariantTrackLoad', 'AnnotationTrackLoad']}, 'ReferenceGenome': {'source': 'class ReferenceGenome(GradioModel):\n id: Optional[str] = Field(default="hg38")\n name: Optional[str] = Field(default="hg38")\n fastaURL: Optional[str] = Field(default=None)\n indexURL: Optional[str] = Field(default=None)\n compressedIndexURL: Optional[str] = Field(default=None)\n twoBitURL: Optional[str] = Field(default=None)\n cytobandURL: Optional[str] = Field(default=None)\n aliasURL: Optional[str] = Field(default=None)\n chromSizesURL: Optional[str] = Field(default=None)\n chromosomeOrder: Optional[list[str]] = Field(\n default=None\n )\n headers: Optional[Dict[str, str]] = Field(default=None)\n wholeGenomeView: bool = Field(default=True)'}, 'AlignmentTrackLoad': {'source': 'class AlignmentTrackLoad(TrackLoad):\n showCoverage: bool = True\n showAlignments: bool = True\n viewAsPairs: bool = False\n pairsSupported: bool = True\n coverageColor: Optional[str] = None\n color: str = "rgb(170, 170, 170)"\n deletionColor: str = "black"\n displayMode: str = Field(\n default="EXPANDED",\n pattern="^(FULL|EXPANDED|SQUISHED)$",\n )\n groupBy: Optional[str] = None\n samplingWindowSize: int = 100\n samplingDepth: int = 100\n readGroup: Optional[str] = None\n sort: Optional[AlignmentSortOptions] = None\n filter: Dict[str, bool | int | list[str]] = None\n showSoftClips: bool = False\n showMismatches: bool = True\n showAllBases: bool = False\n showInsertionText: bool = False\n insertionTextColor: str = "white"\n alignmentRowHeight: int = 14\n squishedRowHeight: int = 3\n colorBy: str = "unexpectedPair"\n insertionColor: str = "rgb(138, 94, 161)"\n negStrandColor: str = "rgba(150, 150, 230, 0.75)"', 'refs': ['AlignmentSortOptions']}, 'AlignmentSortOptions': {'source': 'class AlignmentSortOptions(GradioModel):\n chr: str\n position: int\n direction: Optional[str] = Field(\n default="ASC", pattern="^(ASC|DESC)$"\n )\n option: str\n tag: Optional[str] = None'}, 'VariantTrackLoad': {'source': 'class VariantTrackLoad(TrackLoad):\n displayMode: Optional[str] = Field(\n default="EXPANDED",\n pattern="^(EXPANDED|SQUISHED|COLLAPSED)$",\n )\n squishedCallHeight: Optional[int] = 1\n expandedCallHeight: Optional[int] = 10\n color: Optional[str] = None\n colorBy: Optional[str] = None\n colorTable: Optional[Dict[str, str]] = None\n noCallColor: Optional[str] = "rgb(250, 250, 250)"\n homvarColor: Optional[str] = "rgb(17,248,254)"\n hetvarColor: Optional[str] = "rgb(34,12,253)"\n homrefColor: Optional[str] = "rgb(200, 200, 200)"\n supportsWholeGenome: Optional[bool] = None\n showGenotypes: Optional[bool] = None\n # strokecolor: Optional[Callable[[VCFItem], str]] = None\n # context_hook: Optional[Callable[[VCFItem, Draw.CanvasContext, int, int, int, int], None]] = None'}, 'AnnotationTrackLoad': {'source': 'class AnnotationTrackLoad(TrackLoad):\n displayMode: str = Field(\n default="COLLAPSED",\n pattern="^(EXPANDED|SQUISHED|COLLAPSED)$",\n )\n squishedRowHeight: int = 15\n expandedRowHeight: int = 30\n color: str = "rgb(0,0,150)"\n colorBy: Optional[str] = None\n altColor: Optional[str] = None\n colorTable: Optional[Dict[str, str]] = None\n searchable: bool = False\n searchableFields: list[str] = Field(\n default_factory=list\n )\n nameField: Optional[str] = None\n maxRows: int = 500\n filterTypes: Optional[list[str]] = None'}}, 'user_fn_refs': {'IGV': ['IGVContext']}}} abs_path = os.path.join(os.path.dirname(__file__), "css.css") with gr.Blocks( css=abs_path, theme=gr.themes.Default( font_mono=[ gr.themes.GoogleFont("Inconsolata"), "monospace", ], ), ) as demo: gr.Markdown( """ # `gradio_igv`
Static Badge
Embed IGV.js in your app to visualize genomics data. """, elem_classes=["md-custom"], header_links=True) app.render() gr.Markdown( """ ## Installation ```bash pip install gradio_igv ``` ## Usage ```python import gradio as gr from gradio_igv import IGV, IGVContext, AlignmentTrackLoad, FeatureContext, parse_locus import pandas as pd public_cram = "https://s3.amazonaws.com/1000genomes/data/HG00103/alignment/HG00103.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram" default_igv_context = IGVContext( genome="hg38", ).update_locus("BRCA1").add_track( AlignmentTrackLoad( name="HG00103", url=public_cram, indexURL=f"{public_cram}.crai", order=1, height=200, colorBy="strand", oauthToken=None, # Public file so no auth needed; otherwise inferred by URL type using environment ) ) def summarize_visible_alignments(igv_context): loci = parse_locus(igv_context.locus) feature_ctx = FeatureContext( files=[public_cram], names=["HG00103"], loci=loci, ) reads = list(feature_ctx.features["HG00103"]) df = pd.DataFrame({ "Read Name": [read.query_name for read in reads], "Pos": [read.reference_start for read in reads], "MAPQ": [read.mapq for read in reads], }).sort_values(by='Pos') return df.head(20) with gr.Blocks() as demo: with gr.Row(): with gr.Column(scale=3): igv_component = IGV(value=default_igv_context, label="IGV Browser") with gr.Column(scale=1): alignment_summary = gr.DataFrame(value=pd.DataFrame(), label="Alignment Summary", max_height=800) igv_component.locuschange(summarize_visible_alignments, [igv_component], [alignment_summary]) if __name__ == "__main__": demo.launch() ``` """, elem_classes=["md-custom"], header_links=True) gr.Markdown(""" ## `IGV` ### Initialization """, elem_classes=["md-custom"], header_links=True) gr.ParamViewer(value=_docs["IGV"]["members"]["__init__"], linkify=['IGVContext', 'ReferenceGenome', 'AlignmentTrackLoad', 'AlignmentSortOptions', 'VariantTrackLoad', 'AnnotationTrackLoad']) gr.Markdown("### Events") gr.ParamViewer(value=_docs["IGV"]["events"], linkify=['Event']) gr.Markdown(""" ### User function The impact on the users predict function varies depending on whether the component is used as an input or output for an event (or both). - When used as an Input, the component only impacts the input signature of the user function. - When used as an output, the component only impacts the return signature of the user function. The code snippet below is accurate in cases where the component is used as both an input and an output. ```python def predict( value: IGVContext ) -> IGVContext: return value ``` """, elem_classes=["md-custom", "IGV-user-fn"], header_links=True) code_IGVContext = gr.Markdown(""" ## `IGVContext` ```python class IGVContext(GradioModel): genome: str | ReferenceGenome = Field(default="hg38") locus: str = Field(default="") loadAlignmentTracks: list[AlignmentTrackLoad] = Field( default_factory=list ) loadVariantTracks: list[VariantTrackLoad] = Field( default_factory=list ) loadAnnotationTracks: list[AnnotationTrackLoad] = Field( default_factory=list ) removeTracks: list[str] = Field(default_factory=list) def update_genome(self, genome: str | ReferenceGenome): self.genome = genome return self def update_locus(self, locus: str): self.locus = locus return self def add_track(self, track_load: TrackLoad): if isinstance(track_load, AlignmentTrackLoad): self.loadAlignmentTracks.append(track_load) elif isinstance(track_load, VariantTrackLoad): self.loadVariantTracks.append(track_load) elif isinstance(track_load, AnnotationTrackLoad): self.loadAnnotationTracks.append(track_load) else: raise ValueError( "TrackLoad type not recognized." ) return self def remove_track(self, track: str): self.removeTracks.append(track) return self ```""", elem_classes=["md-custom", "IGVContext"], header_links=True) code_ReferenceGenome = gr.Markdown(""" ## `ReferenceGenome` ```python class ReferenceGenome(GradioModel): id: Optional[str] = Field(default="hg38") name: Optional[str] = Field(default="hg38") fastaURL: Optional[str] = Field(default=None) indexURL: Optional[str] = Field(default=None) compressedIndexURL: Optional[str] = Field(default=None) twoBitURL: Optional[str] = Field(default=None) cytobandURL: Optional[str] = Field(default=None) aliasURL: Optional[str] = Field(default=None) chromSizesURL: Optional[str] = Field(default=None) chromosomeOrder: Optional[list[str]] = Field( default=None ) headers: Optional[Dict[str, str]] = Field(default=None) wholeGenomeView: bool = Field(default=True) ```""", elem_classes=["md-custom", "ReferenceGenome"], header_links=True) code_AlignmentTrackLoad = gr.Markdown(""" ## `AlignmentTrackLoad` ```python class AlignmentTrackLoad(TrackLoad): showCoverage: bool = True showAlignments: bool = True viewAsPairs: bool = False pairsSupported: bool = True coverageColor: Optional[str] = None color: str = "rgb(170, 170, 170)" deletionColor: str = "black" displayMode: str = Field( default="EXPANDED", pattern="^(FULL|EXPANDED|SQUISHED)$", ) groupBy: Optional[str] = None samplingWindowSize: int = 100 samplingDepth: int = 100 readGroup: Optional[str] = None sort: Optional[AlignmentSortOptions] = None filter: Dict[str, bool | int | list[str]] = None showSoftClips: bool = False showMismatches: bool = True showAllBases: bool = False showInsertionText: bool = False insertionTextColor: str = "white" alignmentRowHeight: int = 14 squishedRowHeight: int = 3 colorBy: str = "unexpectedPair" insertionColor: str = "rgb(138, 94, 161)" negStrandColor: str = "rgba(150, 150, 230, 0.75)" ```""", elem_classes=["md-custom", "AlignmentTrackLoad"], header_links=True) code_AlignmentSortOptions = gr.Markdown(""" ## `AlignmentSortOptions` ```python class AlignmentSortOptions(GradioModel): chr: str position: int direction: Optional[str] = Field( default="ASC", pattern="^(ASC|DESC)$" ) option: str tag: Optional[str] = None ```""", elem_classes=["md-custom", "AlignmentSortOptions"], header_links=True) code_VariantTrackLoad = gr.Markdown(""" ## `VariantTrackLoad` ```python class VariantTrackLoad(TrackLoad): displayMode: Optional[str] = Field( default="EXPANDED", pattern="^(EXPANDED|SQUISHED|COLLAPSED)$", ) squishedCallHeight: Optional[int] = 1 expandedCallHeight: Optional[int] = 10 color: Optional[str] = None colorBy: Optional[str] = None colorTable: Optional[Dict[str, str]] = None noCallColor: Optional[str] = "rgb(250, 250, 250)" homvarColor: Optional[str] = "rgb(17,248,254)" hetvarColor: Optional[str] = "rgb(34,12,253)" homrefColor: Optional[str] = "rgb(200, 200, 200)" supportsWholeGenome: Optional[bool] = None showGenotypes: Optional[bool] = None # strokecolor: Optional[Callable[[VCFItem], str]] = None # context_hook: Optional[Callable[[VCFItem, Draw.CanvasContext, int, int, int, int], None]] = None ```""", elem_classes=["md-custom", "VariantTrackLoad"], header_links=True) code_AnnotationTrackLoad = gr.Markdown(""" ## `AnnotationTrackLoad` ```python class AnnotationTrackLoad(TrackLoad): displayMode: str = Field( default="COLLAPSED", pattern="^(EXPANDED|SQUISHED|COLLAPSED)$", ) squishedRowHeight: int = 15 expandedRowHeight: int = 30 color: str = "rgb(0,0,150)" colorBy: Optional[str] = None altColor: Optional[str] = None colorTable: Optional[Dict[str, str]] = None searchable: bool = False searchableFields: list[str] = Field( default_factory=list ) nameField: Optional[str] = None maxRows: int = 500 filterTypes: Optional[list[str]] = None ```""", elem_classes=["md-custom", "AnnotationTrackLoad"], header_links=True) demo.load(None, js=r"""function() { const refs = { IGVContext: ['ReferenceGenome', 'AlignmentTrackLoad', 'VariantTrackLoad', 'AnnotationTrackLoad'], ReferenceGenome: [], AlignmentTrackLoad: ['AlignmentSortOptions'], AlignmentSortOptions: [], VariantTrackLoad: [], AnnotationTrackLoad: [], }; const user_fn_refs = { IGV: ['IGVContext'], }; requestAnimationFrame(() => { Object.entries(user_fn_refs).forEach(([key, refs]) => { if (refs.length > 0) { const el = document.querySelector(`.${key}-user-fn`); if (!el) return; refs.forEach(ref => { el.innerHTML = el.innerHTML.replace( new RegExp("\\b"+ref+"\\b", "g"), `${ref}` ); }) } }) Object.entries(refs).forEach(([key, refs]) => { if (refs.length > 0) { const el = document.querySelector(`.${key}`); if (!el) return; refs.forEach(ref => { el.innerHTML = el.innerHTML.replace( new RegExp("\\b"+ref+"\\b", "g"), `${ref}` ); }) } }) }) } """) demo.launch()