pileup.js component (#543)

* tests work for hard coded reference * tracks can be loaded in, tests passing * tests all pass, demos in progress * clean up * fixed rendering bug in pileup.js * data for RNA-seq demo * added pileup demo image * tests pass * fixed css and cleaned unused styles * demo done * revert dev build * deleted unused files * rebuild async files after merge * review comments * added option to modify visualization options * Apply suggestions from code review Co-authored-by: HammadTheOne <[email protected]> * small documentation fixes * Apply suggestions from code review Co-authored-by: Alex Johnson <[email protected]> * Linting fixes * Fixed layout_helper linting * Rebuilding package * Updated CHANGELOG * Added shared chunk for webpack deps with IGV and Pileup Co-authored-by: HammadTheOne <[email protected]> Co-authored-by: Alex Johnson <[email protected]>
plotly · Apr 1, 2021 · 9e5da85 · 9e5da85
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## Unreleased
+### Added
+* [#543](https://github.com/plotly/dash-bio/pull/543) Added Dash Pileup component.
+
 ## [0.6.1] - 2021-02-15
 ### Fixed
 * [#544](https://github.com/plotly/dash-bio/pull/544) Miscellaneous fixes for NglMoleculeViewer component.

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,4 +1,5 @@
 include dash_bio/bundle.js
+include dash_bio/dash_bio-shared.js
 include dash_bio/async-*.js
 include dash_bio/async-*.js.map
 include dash_bio/metadata.json

diff --git a/NAMESPACE b/NAMESPACE
@@ -10,6 +10,7 @@ export(dashbioMolecule3dViewer)
 export(dashbioNeedlePlot)
 export(dashbioNglMoleculeViewer)
 export(dashbioOncoPrint)
+export(dashbioPileup)
 export(dashbioSequenceViewer)
 export(dashbioSpeck)
 export(dashbioVolcano)

diff --git a/R/dashbioPileup.R b/R/dashbioPileup.R
@@ -0,0 +1,18 @@
+# AUTO GENERATED FILE - DO NOT EDIT
+
+dashbioPileup <- function(id=NULL, style=NULL, className=NULL, range=NULL, reference=NULL, tracks=NULL) {
+
+    props <- list(id=id, style=style, className=className, range=range, reference=reference, tracks=tracks)
+    if (length(props) > 0) {
+        props <- props[!vapply(props, is.null, logical(1))]
+    }
+    component <- list(
+        props = props,
+        type = 'Pileup',
+        namespace = 'dash_bio',
+        propNames = c('id', 'style', 'className', 'range', 'reference', 'tracks'),
+        package = 'dashBio'
+        )
+
+    structure(component, class = c('dash_component', 'list'))
+}
diff --git a/R/internal.R b/R/internal.R
@@ -26,6 +26,12 @@ all_files = FALSE, async = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
 version = "0.6.1", src = list(href = NULL,
 file = "deps"), meta = NULL,
+script = 'async-pileup.js',
+stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
+all_files = FALSE, async = TRUE), class = "html_dependency"),
+`dash_bio` = structure(list(name = "dash_bio",
+version = "0.6.1", src = list(href = NULL,
+file = "deps"), meta = NULL,
 script = 'async-moleculeviewer2.js',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, async = TRUE), class = "html_dependency"),
@@ -92,6 +98,12 @@ all_files = FALSE, dynamic = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
 version = "0.6.1", src = list(href = NULL,
 file = "deps"), meta = NULL,
+script = 'async-pileup.js.map',
+stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
+all_files = FALSE, dynamic = TRUE), class = "html_dependency"),
+`dash_bio` = structure(list(name = "dash_bio",
+version = "0.6.1", src = list(href = NULL,
+file = "deps"), meta = NULL,
 script = 'async-moleculeviewer2.js.map',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, dynamic = TRUE), class = "html_dependency"),
@@ -136,6 +148,12 @@ version = "0.6.1", src = list(href = NULL,
 file = "deps"), meta = NULL,
 script = 'bundle.js',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
-all_files = FALSE), class = "html_dependency"))
+all_files = FALSE), class = "html_dependency"),
+`dash_bio-shared` = structure(list(name = "dash_bio-shared",
+version = "0.6.1", src = list(href = NULL,
+file = "deps"), meta = NULL,
+script = 'dash_bio-shared.js',
+stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
+all_files = FALSE, async = TRUE), class = "html_dependency"))
 return(deps_metadata)
 }
diff --git a/dash_bio/Pileup.py b/dash_bio/Pileup.py
@@ -0,0 +1,62 @@
+# 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'.
+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
+- 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. Must be one of
+            (coverage, genome, genes, features, idiogram, location, scale,
+            variants, genotypes, or pileup)
+            See https://github.com/hammerlab/pileup.js/blob/master/src/main/pileup.js
+  - vizOptions (optional): Options that define viz details.
+            Options depend on the viz type selected.
+  - label (string; optional): Label to display by track
+  - source (optional): Data source to visualize. Must be one of
+            (bam, vcf, alignmentJson, variantJson, featureJson, idiogramJson, cytoBand,
+            vcf, twoBit, bigBed, GAReadAlignment, GAVariant, GAFeature, GAGene)
+            See https://github.com/hammerlab/pileup.js/blob/master/src/main/pileup.js
+  - 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)
diff --git a/dash_bio/__init__.py b/dash_bio/__init__.py
@@ -37,6 +37,7 @@
     'circos',
     'ideogram',
     'igv',
+    'pileup',
     'moleculeviewer2',
     'moleculeviewer3',
     'needle',
@@ -79,6 +80,18 @@
     }
 ])
 
+_js_dist.extend([
+    {
+        'relative_package_path': 'dash_bio-shared.js',
+        'external_url': (
+            'https://unpkg.com/dash-bio@{}'
+            '/' + package_name + '/dash_bio-shared.js'
+        ).format(__version__),
+        'async': True,
+        'namespace': 'dash_bio'
+    }
+])
+
 _css_dist = []
 
 

diff --git a/dash_bio/_imports_.py b/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"
 ]
diff --git a/dash_bio/async-alignment.js b/dash_bio/async-alignment.js
diff --git a/dash_bio/async-circos.js b/dash_bio/async-circos.js
diff --git a/dash_bio/async-ideogram.js b/dash_bio/async-ideogram.js
diff --git a/dash_bio/async-igv.js b/dash_bio/async-igv.js
diff --git a/dash_bio/async-moleculeviewer2.js b/dash_bio/async-moleculeviewer2.js
diff --git a/dash_bio/async-moleculeviewer3.js b/dash_bio/async-moleculeviewer3.js
diff --git a/dash_bio/async-needle.js b/dash_bio/async-needle.js
diff --git a/dash_bio/async-nglmoleculeviewer.js b/dash_bio/async-nglmoleculeviewer.js