pileup.js component

NAMESPACE

@@ -5,6 +5,7 @@ export(dashbioCircos)
 export(dashbioFornaContainer)
 export(dashbioIdeogram)
 export(dashbioIgv)
+export(dashbioPileup)
 export(dashbioMolecule2dViewer)
 export(dashbioMolecule3dViewer)
 export(dashbioNeedlePlot)

dash_bio/Pileup.py

@@ -0,0 +1,59 @@
+# AUTO GENERATED FILE - DO NOT EDIT
+
+from dash.development.base_component import Component, _explicitize_args
+
+
+class Pileup(Component):
+    """A Pileup component.
+The Pileup component is a genome visualization component
+developed by the the Hammerlab. It uses an
+example integration of pileup.js and React (https://www.npmjs.com/package/pileup).
+
+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.
+- style (dict; optional): Generic style overrides on the plot div
+- className (string; optional): className of the component div.
+- range (dict; optional): Object defining genomic location.
+    Of the format: {contig: 'chr17', start: 7512384, stop: 7512544}. range has the following type: dict containing keys 'contig', 'start', 'stop'.
+Those keys have the following types:
+  - contig (string; optional): Name of contig to display. (ie. chr17)
+  - start (number; optional): Start location to display
+  - stop (number; optional): Stop location to display
+- reference (dict; optional): Object defining genomic reference. reference has the following type: dict containing keys 'label', 'url', 'stop'.
+Those keys have the following types:
+  - label (string; optional): Label to display by reference
+  - url (string; optional): Url of 2bit file.
+         https://genome.ucsc.edu/goldenPath/help/twoBit.html
+  - stop (number; optional): Stop location to display
+- tracks (dict; optional): Array of configuration objects defining tracks initially displayed when app launches.
+    see https://github.com/hammerlab/pileup.js#usage. tracks has the following type: list of dicts containing keys 'viz', 'vizOptions', 'label', 'source', 'sourceOptions'.
+Those keys have the following types:
+  - viz (optional): Name of visualization.
+            (ie coverage, genome, genes, etc.)
+  - vizOptions (optional): Options that define viz defails.
+            Options depend on the viz type selected.
+  - label (string; optional): Label to display by track
+  - source (optional): Data source to visualize.
+            (ie bam, vcf, alignmentJson, GAVariant, etc.)
+  - sourceOptions (optional): Options that define data source.
+            Options depend on the source selected."""
+    @_explicitize_args
+    def __init__(self, id=Component.UNDEFINED, style=Component.UNDEFINED, className=Component.UNDEFINED, range=Component.UNDEFINED, reference=Component.UNDEFINED, tracks=Component.UNDEFINED, **kwargs):
+        self._prop_names = ['id', 'style', 'className', 'range', 'reference', 'tracks']
+        self._type = 'Pileup'
+        self._namespace = 'dash_bio'
+        self._valid_wildcard_attributes =            []
+        self.available_properties = ['id', 'style', 'className', 'range', 'reference', 'tracks']
+        self.available_wildcard_properties =            []
+
+        _explicit_args = kwargs.pop('_explicit_args')
+        _locals = locals()
+        _locals.update(kwargs)  # For wildcard attrs
+        args = {k: _locals[k] for k in _explicit_args if k != 'children'}
+
+        for k in []:
+            if k not in args:
+                raise TypeError(
+                    'Required argument `' + k + '` was not specified.')
+        super(Pileup, self).__init__(**args)

dash_bio/__init__.py

@@ -37,6 +37,7 @@
     'circos',
     'ideogram',
     'igv',
+    'pileup',
     'moleculeviewer2',
     'moleculeviewer3',
     'needle',

dash_bio/_imports_.py

@@ -8,6 +8,7 @@
 from .NeedlePlot import NeedlePlot
 from .NglMoleculeViewer import NglMoleculeViewer
 from .OncoPrint import OncoPrint
+from .Pileup import Pileup
 from .SequenceViewer import SequenceViewer
 from .Speck import Speck
 
@@ -22,6 +23,7 @@
     "NeedlePlot",
     "NglMoleculeViewer",
     "OncoPrint",
+    "Pileup",
     "SequenceViewer",
     "Speck"
 ]

dash_bio/metadata.json

@@ -2289,6 +2289,132 @@
       }
     }
   },
+  "src/lib/components/Pileup.react.js": {
+    "description": "The Pileup component is a genome visualization component\ndeveloped by the the Hammerlab. It uses an\nexample integration of pileup.js and React (https://www.npmjs.com/package/pileup).",
+    "displayName": "Pileup",
+    "methods": [],
+    "props": {
+      "id": {
+        "type": {
+          "name": "string"
+        },
+        "required": false,
+        "description": "The ID of this component, used to identify dash components in callbacks.\nThe ID needs to be unique across all of the components in an app."
+      },
+      "setProps": {
+        "type": {
+          "name": "func"
+        },
+        "required": false,
+        "description": "Dash-assigned callback that should be called to report property changes\nto Dash, to make them available for callbacks."
+      },
+      "style": {
+        "type": {
+          "name": "object"
+        },
+        "required": false,
+        "description": "Generic style overrides on the plot div"
+      },
+      "className": {
+        "type": {
+          "name": "string"
+        },
+        "required": false,
+        "description": "className of the component div."
+      },
+      "range": {
+        "type": {
+          "name": "exact",
+          "value": {
+            "contig": {
+              "name": "string",
+              "description": "Name of contig to display. (ie. chr17)",
+              "required": false
+            },
+            "start": {
+              "name": "number",
+              "description": "Start location to display",
+              "required": false
+            },
+            "stop": {
+              "name": "number",
+              "description": "Stop location to display",
+              "required": false
+            }
+          }
+        },
+        "required": false,
+        "description": "Object defining genomic location.\n    Of the format: {contig: 'chr17', start: 7512384, stop: 7512544}"
+      },
+      "reference": {
+        "type": {
+          "name": "shape",
+          "value": {
+            "label": {
+              "name": "string",
+              "description": "Label to display by reference",
+              "required": false
+            },
+            "url": {
+              "name": "string",
+              "description": "Url of 2bit file.\n         https://genome.ucsc.edu/goldenPath/help/twoBit.html",
+              "required": false
+            },
+            "stop": {
+              "name": "number",
+              "description": "Stop location to display",
+              "required": false
+            }
+          }
+        },
+        "required": false,
+        "description": "Object defining genomic reference."
+      },
+      "tracks": {
+        "type": {
+          "name": "arrayOf",
+          "value": {
+            "name": "shape",
+            "value": {
+              "viz": {
+                "name": "enum",
+                "computed": true,
+                "value": "PILEUP_VIZ_TYPES",
+                "description": "Name of visualization.\n            (ie coverage, genome, genes, etc.)",
+                "required": false
+              },
+              "vizOptions": {
+                "name": "custom",
+                "raw": "PropTypes.Object",
+                "description": "Options that define viz defails.\n            Options depend on the viz type selected.",
+                "required": false
+              },
+              "label": {
+                "name": "string",
+                "description": "Label to display by track",
+                "required": false
+              },
+              "source": {
+                "name": "enum",
+                "computed": true,
+                "value": "PILEUP_SOURCE_TYPES",
+                "description": "Data source to visualize.\n            (ie bam, vcf, alignmentJson, GAVariant, etc.)",
+                "required": false
+              },
+              "sourceOptions": {
+                "name": "custom",
+                "raw": "PropTypes.Object",
+                "description": "Options that define data source.\n            Options depend on the source selected.",
+                "required": false
+              }
+            }
+          }
+        },
+        "required": false,
+        "description": "Array of configuration objects defining tracks initially displayed when app launches.\n    see https://github.com/hammerlab/pileup.js#usage"
+      }
+    }
+  },
   "src/lib/components/SequenceViewer.react.js": {
     "description": "The sequence viewer component is used to display sequences\nthat represent proteins, strands of genomic information, and\nmore. It can apply a coverage to the sequence supplied (with\nclickable coverage sections that can display specific information,\nand an optional legend to describe the color codes used),\nsearch through the sequence for specific regex, capture\nmouse selection events of subparts of the sequence, display a\ncount of the number of nucleotides or amino acids in the\nsequence,\nRead more about the component here:\nhttps://github.com/FlyBase/react-sequence-viewer",
     "displayName": "SequenceViewer",
@@ -2730,4 +2856,4 @@
       }
     }
   }
-}
+}

dash_bio/package-info.json

@@ -1,94 +1 @@
-{
-  "name": "dash-bio",
-  "version": "0.6.1",
-  "description": "Dash components for bioinformatics",
-  "repository": {
-    "type": "git",
-    "url": "[email protected]:plotly/dash-bio.git"
-  },
-  "bugs": {
-    "url": "https://github.com/plotly/dash-bio/issues"
-  },
-  "homepage": "https://github.com/plotly/dash-bio",
-  "main": "build/index.js",
-  "scripts": {
-    "format:test": "prettier --config .prettierrc --list-different \"{src/**/, src/lib/components/}*.js\"",
-    "format": "prettier --config .prettierrc --write \"{src/**/, src/lib/components/}*.js\"",
-    "lint:test": "eslint src",
-    "lint": "eslint src --fix",
-    "test": "npm run lint:test && npm run format:test && npm run test-unit",
-    "test-unit": "jest",
-    "build:js-dev": "webpack --mode development",
-    "build:js": "npm run lint && npm run format && webpack --mode production",
-    "build:py": "node ./extract-meta src/lib/components > dash_bio/metadata.json && python get_version_info.py && python -c \"import dash; dash.development.component_loader.generate_classes('dash_bio', 'dash_bio/metadata.json')\"",
-    "build:r": "dash-generate-components ./src/lib/components dash_bio -p package-info.json --r-prefix='dashbio' --r-imports='dash' --r-depends='manhattanly'",
-    "build": "npm run build:js && npm run build:py",
-    "build:all": "npm run build && npm run build:r",
-    "postbuild": "es-check es5 dash_bio/*.js",
-    "build:dev": "npm run build:js-dev && npm run build:py"
-  },
-  "author": "The Plotly Team <[email protected]>",
-  "maintainer": "Ryan Patrick Kyle <[email protected]>",
-  "license": "MIT",
-  "dependencies": {
-    "circos": "git+https://github.com/plotly/circosJS.git#matthewchan15-zoom-pan-svg",
-    "fast-memoize": "^2.5.1",
-    "fornac": "git://github.com/plotly/fornac.git#6b1b84740d35bf37ca7d251e665039a87b4c2ea9",
-    "ideogram": "git+https://github.com/eweitz/ideogram.git#7d9b2ab91b91ef35db93bdeb529d4760de63292f",
-    "igv": "2.6.8",
-    "molecule-2d-for-react": "git://github.com/plotly/molecule-2d-for-react.git",
-    "molecule-3d-for-react": "git://github.com/plotly/molecule-3d-for-react.git",
-    "ngl": "^0.10.4",
-    "plotly.js": "^1.52.2",
-    "ramda": "^0.26.0",
-    "react": "16.13.0",
-    "react-alignment-viewer": "^0.5.5",
-    "react-dom": "16.13.0",
-    "react-oncoprint": "^1.2.3",
-    "react-plotly.js": "^2.4.0",
-    "react-sequence-viewer": "git://github.com/plotly/react-sequence-viewer.git",
-    "speck": "git://github.com/plotly/speck.git"
-  },
-  "devDependencies": {
-    "@babel/core": "^7.8.4",
-    "@babel/plugin-syntax-dynamic-import": "^7.8.3",
-    "@babel/preset-env": "^7.8.4",
-    "@babel/preset-react": "^7.8.3",
-    "@plotly/webpack-dash-dynamic-import": "^1.1.5",
-    "babel-eslint": "^10.0.3",
-    "babel-jest": "^24.5.0",
-    "babel-loader": "^8.0.6",
-    "copyfiles": "^2.2.0",
-    "css-loader": "^3.4.2",
-    "enzyme": "^3.11.0",
-    "enzyme-adapter-react-16": "^1.15.2",
-    "es-check": "^5.0.0",
-    "eslint": "^6.8.0",
-    "eslint-config-prettier": "^6.10.0",
-    "eslint-plugin-import": "^2.20.1",
-    "eslint-plugin-prettier": "^3.1.2",
-    "eslint-plugin-react": "^7.18.3",
-    "jest": "^24.5.0",
-    "jest-canvas-mock": "^2.2.0",
-    "jest-raw-loader": "^1.0.1",
-    "prettier": "^1.19.1",
-    "react-docgen": "^3.0.0",
-    "react-test-renderer": "^16.12.0",
-    "style-loader": "^0.23.0",
-    "webpack": "^4.41.5",
-    "webpack-cli": "^3.3.10",
-    "webpack-serve": "^3.2.0"
-  },
-  "peerDependencies": {
-    "react": ">=0.14",
-    "react-dom": ">=0.14"
-  },
-  "files": [
-    "dash_bio/bundle.js",
-    "dash_bio/async~*.js"
-  ],
-  "engines": {
-    "node": ">=8.11.0",
-    "npm": ">=6.1.0"
-  }
-}
+{"name": "dash_bio", "version": "0.6.1", "author": "The Plotly Team <[email protected]>"}