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shitohana · Dec 29, 2023 · eda082e · eda082e
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diff --git a/docs_copy/_binom.rst → docs/_binom.rst b/docs_copy/_binom.rst → docs/_binom.rst
diff --git a/docs_copy/_genome.rst → docs/_genome.rst b/docs_copy/_genome.rst → docs/_genome.rst
diff --git a/docs_copy/_metagene.rst → docs/_metagene.rst b/docs_copy/_metagene.rst → docs/_metagene.rst
diff --git a/docs_copy/_plots.rst → docs/_plots.rst b/docs_copy/_plots.rst → docs/_plots.rst
diff --git a/docs/_templates/autosummary/module.rst b/docs/_templates/autosummary/module.rst
diff --git a/docs_copy/_templates/class.rst → docs/_templates/class.rst b/docs_copy/_templates/class.rst → docs/_templates/class.rst
@@ -16,8 +16,10 @@
     :template: method.rst
    {% for item in methods %}
       {% if item != "__init__" %}
+      {%- if item not in inherited_members %}
          ~{{ name }}.{{ item }}
       {% endif %}
+      {% endif %}
    {%- endfor %}
    {% endif %}
    {% endblock %}
diff --git a/docs_copy/_templates/class_native.rst → docs/_templates/class_native.rst b/docs_copy/_templates/class_native.rst → docs/_templates/class_native.rst
diff --git a/docs_copy/_templates/method.rst → docs/_templates/method.rst b/docs_copy/_templates/method.rst → docs/_templates/method.rst
diff --git a/docs/_templates/module.rst b/docs/_templates/module.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,30 +1,35 @@
+import os
+import sys
+
 project = 'BismarkPlot'
 copyright = '2023, shitohana'
 author = 'shitohana'
-release = '1.2'
-import os
-import sys
+release = '1.4.1'
 sys.path.insert(0, os.path.abspath('../src'))
 sys.path.insert(0, os.path.abspath('../src/bismarkplot'))
 sys.path.append(os.path.abspath('.'))
 
-
 extensions = [
+    # TODO add myst_parser to dependencies
+    'myst_parser',
+    'sphinx.ext.intersphinx',
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
-    'sphinx_autodoc_typehints',
     'sphinx.ext.napoleon'
 ]
 
 templates_path = ['_templates']
-autodoc_mock_imports = ['polars', 'matplotlib', 'numpy', 'scipy', 'pandas', 'pyarrow', 'pyreadr', 'dynamicTreeCut']
+autodoc_mock_imports = ['polars', 'matplotlib', 'numpy', 'scipy', 'pandas', 'pyarrow', 'pyreadr', 'dynamicTreeCut', 'plotly', 'numba', 'pathlib']
 autodoc_default_options = {
     'members': True,
-    # 'exclude-members': '__init__'
+    'exclude-members': '__init__'
 }
 autosummary_generate = True
+autodoc_member_order = 'bysource'
 add_module_names = False
 html_short_title = 'BismarkPlot Documentation'
 
 
-html_theme = 'sphinx_book_theme'
+html_theme = 'sphinx_rtd_theme'
+html_show_sourcelink = False
+
diff --git a/..._copy/images/boxplot/bp_ara_bradi_mpl.png → docs/images/boxplot/bp_ara_bradi_mpl.png b/..._copy/images/boxplot/bp_ara_bradi_mpl.png → docs/images/boxplot/bp_ara_bradi_mpl.png
diff --git a/...py/images/boxplot/bp_ara_bradi_plotly.png → docs/images/boxplot/bp_ara_bradi_plotly.png b/...py/images/boxplot/bp_ara_bradi_plotly.png → docs/images/boxplot/bp_ara_bradi_plotly.png
diff --git a/.../boxplot/bp_ara_bradi_plotly_nofilter.png → .../boxplot/bp_ara_bradi_plotly_nofilter.png b/.../boxplot/bp_ara_bradi_plotly_nofilter.png → .../boxplot/bp_ara_bradi_plotly_nofilter.png
diff --git a/..._copy/images/boxplot/vp_ara_bradi_mpl.png → docs/images/boxplot/vp_ara_bradi_mpl.png b/..._copy/images/boxplot/vp_ara_bradi_mpl.png → docs/images/boxplot/vp_ara_bradi_mpl.png
diff --git a/docs/images/boxplot/vp_ara_bradi_plotly.png b/docs/images/boxplot/vp_ara_bradi_plotly.png
diff --git a/docs_copy/images/heatmap/ara_bradi_mpl.png → docs/images/heatmap/ara_bradi_mpl.png b/docs_copy/images/heatmap/ara_bradi_mpl.png → docs/images/heatmap/ara_bradi_mpl.png
diff --git a/..._copy/images/heatmap/ara_bradi_plotly.png → docs/images/heatmap/ara_bradi_plotly.png b/..._copy/images/heatmap/ara_bradi_plotly.png → docs/images/heatmap/ara_bradi_plotly.png
diff --git a/docs_copy/images/heatmap/ara_mpl.png → docs/images/heatmap/ara_mpl.png b/docs_copy/images/heatmap/ara_mpl.png → docs/images/heatmap/ara_mpl.png
diff --git a/docs_copy/images/heatmap/ara_plotly.png → docs/images/heatmap/ara_plotly.png b/docs_copy/images/heatmap/ara_plotly.png → docs/images/heatmap/ara_plotly.png
diff --git a/docs/images/lineplot/ara_NO_major_labels.png b/docs/images/lineplot/ara_NO_major_labels.png
diff --git a/docs/images/lineplot/ara_NO_minor_labels.png b/docs/images/lineplot/ara_NO_minor_labels.png
diff --git a/docs/images/lineplot/ara_bradi_mpl.png b/docs/images/lineplot/ara_bradi_mpl.png
diff --git a/...copy/images/lineplot/ara_bradi_plotly.png → docs/images/lineplot/ara_bradi_plotly.png b/...copy/images/lineplot/ara_bradi_plotly.png → docs/images/lineplot/ara_bradi_plotly.png
diff --git a/docs/images/lineplot/ara_custom_label.png b/docs/images/lineplot/ara_custom_label.png
diff --git a/docs/images/lineplot/ara_major_labels.png b/docs/images/lineplot/ara_major_labels.png
diff --git a/docs/images/lineplot/ara_minor_labels.png b/docs/images/lineplot/ara_minor_labels.png
diff --git a/docs_copy/images/lineplot/ara_multi_mpl.png → docs/images/lineplot/ara_multi_mpl.png b/docs_copy/images/lineplot/ara_multi_mpl.png → docs/images/lineplot/ara_multi_mpl.png
diff --git a/...copy/images/lineplot/ara_multi_plotly.png → docs/images/lineplot/ara_multi_plotly.png b/...copy/images/lineplot/ara_multi_plotly.png → docs/images/lineplot/ara_multi_plotly.png
diff --git a/docs_copy/images/lineplot/ara_mpl.png → docs/images/lineplot/lp_ara_mpl.png b/docs_copy/images/lineplot/ara_mpl.png → docs/images/lineplot/lp_ara_mpl.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -2,17 +2,18 @@ Welcome to BismarkPlot's documentation!
 =======================================
 This page gives an overview of all public objects, functions and methods.
 
+
 .. toctree::
+    :caption: Tutorials
+
+    markdowns/test
 
-.. autosummary::
-    :toctree: _autosummary
-    :template: module.rst
 
-    BismarkPlot.Metagene
-    BismarkPlot.MetageneFiles
-    BismarkPlot.Genome
-    BismarkPlot.ChrLevels
-    BismarkPlot.Clustering
-    BismarkPlot.BismarkBase
-    BismarkPlot.LinePlot
-    BismarkPlot.HeatMap
+.. toctree::
+    :caption: Reference
+    :maxdepth: 1
+
+    _metagene
+    _plots
+    _binom
+    _genome
diff --git a/docs/markdowns/test.md b/docs/markdowns/test.md
@@ -0,0 +1,128 @@
+# LinePlot Tutorial
+
+This tutorial will explain you how to calculate, visualize and configure line-plots.
+
+## Single metagene
+
+### Initialization
+
+```python
+from bismarkplot import *
+
+# Firstly, we need to read the regions annotation (e.g. reference genome .gff)
+genome = Genome.from_gff("path/to/genome.gff")
+# Next we need to filter regions of interest from the genome
+genes = genome.gene_body(min_length=0, flank_length=2000)
+
+# Now we need to calculate metagene data (e.g. from Bismark output)
+metagene = bismarkplot.Metagene.from_bismark(
+    file="path/to/CX_report.txt",
+    genome=genes,  # filtered regions
+    up_windows=500,
+    body_windows=1000,
+    down_windows=500
+)
+
+# Our metagene contains all methylation contexts and both strands, so we need to filter it 
+# (OPTIONAL for line-plot)
+filtered = metagene.filter(context="CG", strand="+")
+
+# LinePlot now can be created
+lp = filtered.line_plot()
+```
+
+### Basic usage
+
+The easiest way to get the plot is to call `.draw_mpl()` or `.draw_plotly()` methods to get matplotlib and Plotly
+versions of plots respectively
+
+```python
+figure = lp.draw_mpl()
+figure.show()
+```
+
+![basic line-plot mpl](../images/lineplot/lp_ara_mpl.png)
+
+Or for Plotly version
+
+```python
+figure = lp.draw_mpl()
+figure.show()
+```
+
+#### No Metagene filtering
+
+If metagene was not filtered by context, line-plot for all contexts on the same figure will be created
+
+```python
+lp = metagene.line_plot()  # Metagene from previous example
+
+figure = lp.draw_mpl()
+figure.show()
+```
+
+![multi line-plot mpl](../images/lineplot/ara_multi_mpl.png)
+
+And for plotly version
+
+```python
+figure = lp.draw_mpl()
+figure.show()
+```
+
+![multi line-plot plotly](../images/lineplot/ara_multi_plotly.png)
+
+
+### Advanced configuration
+
+Examples for matplotlib version of plots will be shown, but Plotly version is identical.
+
+For all examples we use [metagene filtered by CG context](#initialization).
+
+#### `label` parameter
+
+Custom label can be set for line-plot using `label` parameter:
+
+```python
+lp.draw_mpl(label="My custom label")
+```
+
+![line-plot mpl label](../images/lineplot/ara_custom_label.png)
+
+#### `minor_labels` parameter
+
+Labels for upstream, body and downstream regions can be changed to custom, but **exactly 3** need to be provided. 
+
+Set ``[]`` to disable.
+
+
+```python
+lp.draw_mpl(minor_labels=["-2000kb", "Gene", "+2000kb"])
+```
+
+![line-plot mpl label](../images/lineplot/ara_minor_labels.png)
+
+```python
+lp.draw_mpl(minor_labels=[])
+```
+
+![line-plot mpl label](../images/lineplot/ara_NO_minor_labels.png)
+
+#### `major_labels` parameter
+
+Labels for body region start and end (e.g. TSS, TES) can be changed to custom, but **exactly 2** need to be provided. 
+
+Set ``[]`` to disable.
+
+
+```python
+lp.draw_mpl(major_labels=["Start", "End"], minor_labels=[])
+```
+
+![line-plot mpl label](../images/lineplot/ara_major_labels.png)
+
+```python
+lp.draw_mpl(major_labels=[], minor_labels=["-2000kb", "Gene", "+2000kb"])
+```
+
+![line-plot mpl label](../images/lineplot/ara_NO_major_labels.png)
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -17,3 +17,5 @@ typing-extensions==4.5.0
 tzdata==2023.3
 sphinx_autodoc_typehints==1.23.0
 sphinx_book_theme==1.0.1
+myst-parser==2.0.0
+
diff --git a/docs_copy/.nojekyll b/docs_copy/.nojekyll
diff --git a/docs_copy/Makefile b/docs_copy/Makefile
diff --git a/docs_copy/_Binom/_method/bismarkplot.BinomialData.preprocess.rst b/docs_copy/_Binom/_method/bismarkplot.BinomialData.preprocess.rst
diff --git a/docs_copy/_Binom/_method/bismarkplot.BinomialData.region_pvalue.rst b/docs_copy/_Binom/_method/bismarkplot.BinomialData.region_pvalue.rst
diff --git a/docs_copy/_Binom/_method/bismarkplot.RegionStat.categorise.rst b/docs_copy/_Binom/_method/bismarkplot.RegionStat.categorise.rst
diff --git a/docs_copy/_Binom/_method/bismarkplot.RegionStat.filter.rst b/docs_copy/_Binom/_method/bismarkplot.RegionStat.filter.rst
diff --git a/docs_copy/_Binom/_method/bismarkplot.RegionStat.from_expanded.rst b/docs_copy/_Binom/_method/bismarkplot.RegionStat.from_expanded.rst
diff --git a/docs_copy/_Binom/_method/bismarkplot.RegionStat.save.rst b/docs_copy/_Binom/_method/bismarkplot.RegionStat.save.rst
diff --git a/docs_copy/_Binom/bismarkplot.BinomialData.rst b/docs_copy/_Binom/bismarkplot.BinomialData.rst
diff --git a/docs_copy/_Binom/bismarkplot.RegionStat.rst b/docs_copy/_Binom/bismarkplot.RegionStat.rst
diff --git a/docs_copy/_Genome/_method/bismarkplot.Genome.all.rst b/docs_copy/_Genome/_method/bismarkplot.Genome.all.rst
diff --git a/docs_copy/_Genome/_method/bismarkplot.Genome.cds.rst b/docs_copy/_Genome/_method/bismarkplot.Genome.cds.rst
diff --git a/docs_copy/_Genome/_method/bismarkplot.Genome.exon.rst b/docs_copy/_Genome/_method/bismarkplot.Genome.exon.rst
diff --git a/docs_copy/_Genome/_method/bismarkplot.Genome.from_custom.rst b/docs_copy/_Genome/_method/bismarkplot.Genome.from_custom.rst
diff --git a/docs_copy/_Genome/_method/bismarkplot.Genome.from_gff.rst b/docs_copy/_Genome/_method/bismarkplot.Genome.from_gff.rst
diff --git a/docs_copy/_Genome/_method/bismarkplot.Genome.gene_body.rst b/docs_copy/_Genome/_method/bismarkplot.Genome.gene_body.rst
diff --git a/docs_copy/_Genome/_method/bismarkplot.Genome.near_TES.rst b/docs_copy/_Genome/_method/bismarkplot.Genome.near_TES.rst