dash-bio docs posts

CHANGELOG.md

@@ -2,6 +2,17 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [next] - ???
+
+### Added
+  - dash-bio posts in /doc/python/{alignment-chart.md,circos.md,clustergram.md,molecular-visualizations.md,volacano-plot.md}
+
+### Fixed
+  - Fixed error when serializing dict with mix of string and non-string keys [#3380](https://github.com/plotly/plotly.py/issues/3380)
+
+### Updated
+  - The JSON serialization engines no longer sort their keys [#3380](https://github.com/plotly/plotly.py/issues/3380)
+
 ## [5.3.1] - 2021-08-31
 
 ### Updated

doc/python/bio-alignment-chart.md

@@ -0,0 +1,55 @@
+---
+jupyter:
+  jupytext:
+    notebook_metadata_filter: all
+    text_representation:
+      extension: .md
+      format_name: markdown
+      format_version: '1.3'
+      jupytext_version: 1.13.0
+  kernelspec:
+    display_name: Python 3 (ipykernel)
+    language: python
+    name: python3
+  language_info:
+    codemirror_mode:
+      name: ipython
+      version: 3
+    file_extension: .py
+    mimetype: text/x-python
+    name: python
+    nbconvert_exporter: python
+    pygments_lexer: ipython3
+    version: 3.9.7
+  plotly:
+    display_as: bio
+    language: python
+    layout: base
+    name: Alignment Chart
+    order: 1
+    page_type: u-guide
+    permalink: python/alignment-chart/
+    thumbnail: thumbnail/alignment-chart.png
+---
+
+## Bar Chart for conservation visualization
+
+```python
+import plotly.express as px
+
+df = (pd.read_csv('https://raw.githubusercontent.com/plotly/dash-bio-docs-files/master/gene_conservation.csv')
+        .set_index('0')
+        .loc[['consensus','conservation']]
+        .T)
+
+fig = px.bar(df, labels={ 'index': 'base' }, hover_name='consensus', y='conservation')
+fig.show()
+```
+
+## Alignment Chart in dash_bio
+
+```python no_display=true
+from IPython.display import IFrame
+snippet_url = 'https://dash-gallery.plotly.host/python-docs-dash-snippets/'
+IFrame(snippet_url + 'bio-alignmentchart', width='100%', height=630)
+```

doc/python/bio-circos.md

@@ -0,0 +1,115 @@
+---
+jupyter:
+  jupytext:
+    notebook_metadata_filter: all
+    text_representation:
+      extension: .md
+      format_name: markdown
+      format_version: '1.3'
+      jupytext_version: 1.13.0
+  kernelspec:
+    display_name: Python 3 (ipykernel)
+    language: python
+    name: python3
+  language_info:
+    codemirror_mode:
+      name: ipython
+      version: 3
+    file_extension: .py
+    mimetype: text/x-python
+    name: python
+    nbconvert_exporter: python
+    pygments_lexer: ipython3
+    version: 3.9.7
+  plotly:
+    display_as: bio
+    language: python
+    layout: base
+    name: Clustergram
+    order: 1
+    page_type: u-guide
+    permalink: python/clustergram/
+    thumbnail: thumbnail/clustergram.png
+---
+
+## Default Clustergram
+An example of a default Clustergram component without any extra properties.
+
+
+```python
+import pandas as pd
+import dash_bio
+
+
+df = pd.read_csv(
+    'https://raw.githubusercontent.com/plotly/datasets/master/Dash_Bio/Chromosomal/' +
+    'clustergram_brain_cancer.csv', 
+)
+
+dash_bio.Clustergram(
+    data=df,
+    column_labels=list(df.columns.values),
+    row_labels=list(df.index),
+    height=800,
+    width=700
+)
+```
+
+## Dendrogram Cluster Colors/Line Widths
+Change the colors of the dendrogram traces that are used to represent clusters, and configure their line widths.
+
+
+```python
+import pandas as pd
+import dash_bio
+
+df = pd.read_csv(
+    'https://raw.githubusercontent.com/plotly/datasets/master/Dash_Bio/Chromosomal/' +
+    'clustergram_brain_cancer.csv', 
+)
+
+dash_bio.Clustergram(
+    data=df,
+    column_labels=list(df.columns.values),
+    row_labels=list(df.index),
+    height=800,
+    width=700,
+    color_list={
+        'row': ['#636EFA', '#00CC96', '#19D3F3'],
+        'col': ['#AB63FA', '#EF553B'],
+        'bg': '#506784'
+    },
+    line_width=2
+)
+```
+
+## Relative Dendrogram Size
+Change the relative width and height of, respectively, the row and column dendrograms compared to the width and height of the heatmap.
+
+
+```python
+import pandas as pd
+import dash_bio
+
+df = pd.read_csv(
+    'https://raw.githubusercontent.com/plotly/datasets/master/Dash_Bio/Chromosomal/' +
+    'clustergram_brain_cancer.csv', 
+)
+
+dash_bio.Clustergram(
+    data=df,
+    column_labels=list(df.columns.values),
+    row_labels=list(df.index),
+    height=800,
+    width=700,
+    display_ratio=[0.1, 0.7]
+)
+```
+
+## Circos with Dash
+
+```python no_display=true
+from IPython.display import IFrame
+snippet_url = 'https://dash-gallery.plotly.host/python-docs-dash-snippets/'
+IFrame(snippet_url + 'bio-circos', width='100%', height=630)
+```

doc/python/bio-manhattanplot.md

@@ -0,0 +1,76 @@
+---
+jupyter:
+  celltoolbar: Tags
+  jupytext:
+    notebook_metadata_filter: all
+    text_representation:
+      extension: .md
+      format_name: markdown
+      format_version: '1.3'
+      jupytext_version: 1.13.0
+  kernelspec:
+    display_name: Python 3 (ipykernel)
+    language: python
+    name: python3
+  language_info:
+    codemirror_mode:
+      name: ipython
+      version: 3
+    file_extension: .py
+    mimetype: text/x-python
+    name: python
+    nbconvert_exporter: python
+    pygments_lexer: ipython3
+    version: 3.9.7
+  plotly:
+    display_as: bio
+    language: python
+    layout: base
+    name: Volcano plot
+    order: 1
+    page_type: u-guide
+    permalink: python/volcano-plot/
+    thumbnail: thumbnail/volcano-plot.png
+---
+
+## Manhattan Plot
+
+An example of a default ManhattanPlot component without any extra properties.
+
+```python
+import pandas as pd
+import dash_bio as dashbio
+
+df = pd.read_csv('https://raw.githubusercontent.com/plotly/dash-bio-docs-files/master/manhattan_data.csv')
+
+
+dashbio.ManhattanPlot(
+    dataframe=df,
+)
+```
+
+## Highlighted points color, and colors of the suggestive line and the genome-wide line.
+Change the color of the points that are considered significant.
+
+```python
+import pandas as pd
+import dash_bio as dashbio
+
+
+df = pd.read_csv('https://raw.githubusercontent.com/plotly/dash-bio-docs-files/master/manhattan_data.csv')
+
+dashbio.ManhattanPlot(
+    dataframe=df,
+    highlight_color='#00FFAA',
+    suggestiveline_color='#AA00AA',
+    genomewideline_color='#AA5500'
+)
+```
+
+## ManhattanPlot with Dash
+
+```python no_display=true
+from IPython.display import IFrame
+snippet_url = 'https://dash-gallery.plotly.host/python-docs-dash-snippets/'
+IFrame(snippet_url + 'bio-manhattanplot', width='100%', height=630)
+```

doc/python/bio-volcano-plot.md

@@ -0,0 +1,79 @@
+---
+jupyter:
+  celltoolbar: Tags
+  jupytext:
+    notebook_metadata_filter: all
+    text_representation:
+      extension: .md
+      format_name: markdown
+      format_version: '1.3'
+      jupytext_version: 1.13.0
+  kernelspec:
+    display_name: Python 3 (ipykernel)
+    language: python
+    name: python3
+  language_info:
+    codemirror_mode:
+      name: ipython
+      version: 3
+    file_extension: .py
+    mimetype: text/x-python
+    name: python
+    nbconvert_exporter: python
+    pygments_lexer: ipython3
+    version: 3.9.7
+  plotly:
+    display_as: bio
+    language: python
+    layout: base
+    name: Volcano plot
+    order: 1
+    page_type: u-guide
+    permalink: python/volcano-plot/
+    thumbnail: thumbnail/volcano-plot.png
+---
+
+## VolcanoPlot
+An example of a default VolcanoPlot component without any extra properties.
+
+
+```python
+import pandas as pd
+import dash_bio 
+
+
+df = pd.read_csv(
+    'https://raw.githubusercontent.com/plotly/dash-bio-docs-files/master/' +
+    'volcano_data1.csv'
+)
+
+dash_bio.VolcanoPlot(
+    dataframe=df,
+)
+```
+
+## Point Sizes And Line Widths
+Change the size of the points on the scatter plot, and the widths of the effect lines and genome-wide line.
+
+
+```python
+import pandas as pd
+import dash_bio as dashbio
+
+df = pd.read_csv('https://raw.githubusercontent.com/plotly/dash-bio-docs-files/master/volcano_data1.csv')
+
+dashbio.VolcanoPlot(
+    dataframe=df,
+    point_size=10,
+    effect_size_line_width=4,
+    genomewideline_width=2
+)
+```
+
+## VolcanoPlot with Dash
+
+```python no_display=true
+from IPython.display import IFrame
+snippet_url = 'https://dash-gallery.plotly.host/python-docs-dash-snippets/'
+IFrame(snippet_url + 'bio-volcano', width='100%', height=630)
+```

doc/requirements.txt

@@ -1,5 +1,6 @@
 plotly==5.3.1
 jupytext==1.1.1
+jupyter-client<7
 jupyter
 notebook
 pandas==1.0.3
@@ -32,3 +33,4 @@ pooch
 wget
 nbconvert==5.6.1
 orjson
+dash-bio

packages/python/plotly/plotly/io/_json.py

@@ -112,7 +112,7 @@ def to_json_plotly(plotly_object, pretty=False, engine=None):
     # Dump to a JSON string and return
     # --------------------------------
     if engine == "json":
-        opts = {"sort_keys": True}
+        opts = {}
         if pretty:
             opts["indent"] = 2
         else:
@@ -124,7 +124,7 @@ def to_json_plotly(plotly_object, pretty=False, engine=None):
         return json.dumps(plotly_object, cls=PlotlyJSONEncoder, **opts)
     elif engine == "orjson":
         JsonConfig.validate_orjson()
-        opts = orjson.OPT_SORT_KEYS | orjson.OPT_SERIALIZE_NUMPY
+        opts = orjson.OPT_NON_STR_KEYS | orjson.OPT_SERIALIZE_NUMPY
 
         if pretty:
             opts |= orjson.OPT_INDENT_2
@@ -462,7 +462,7 @@ def clean_to_json_compatible(obj, **kwargs):
         return obj
 
     if isinstance(obj, dict):
-        return {str(k): clean_to_json_compatible(v, **kwargs) for k, v in obj.items()}
+        return {k: clean_to_json_compatible(v, **kwargs) for k, v in obj.items()}
     elif isinstance(obj, (list, tuple)):
         if obj:
             # Must process list recursively even though it may be slow

packages/python/plotly/plotly/tests/test_core/test_graph_objs/test_template.py

@@ -356,7 +356,7 @@ def test_move_nested_trace_properties(self):
             },
         )
 
-        self.assertEqual(pio.to_json(templated_fig), pio.to_json(expected_fig))
+        self.assertEqual(templated_fig.to_dict(), expected_fig.to_dict())
 
     def test_move_nested_trace_properties_existing_traces(self):
         fig = go.Figure(