From f587a63ba268841ef3998f8cfbe6705d21fd5f94 Mon Sep 17 00:00:00 2001
From: shitohana <43905117+shitohana@users.noreply.github.com>
Date: Fri, 29 Dec 2023 15:32:47 +0300
Subject: [PATCH] Plotly (#8)
* Clusters added into master (#6)
* flank regions fix
* new labels
* draw to cluster
* __init__.py Clustering added
BismarkPlot.py Clustering done and confidence bands
console_metagene.py confidence bands added
index.rst new classes and methods added in documentation
* documentation fix
* documentation fix
* v1.2.2 release
* v1.2.2 release
* v1.2.3 release
* v1.2.3 release
* v1.3
* console_chrs.py fixed path
BismarkPlot.py Genome.__trim_genes take flank length anyway
LinePlot added all contexts support
* console_metagene.py empty genome check
* BismarkPlot.py cpu check
console_metagene.py and console_chrs.py file_format fix
* v1.3.0a
* BismarkPlot.py fix cpu_count
console fix dpi, plot types
* v1.3.0a1
* v1.3.0b0
* v1.3.1
* Update README.md
* Update README.md
* Update README.md
* add_flank_lines for heatmap into method
added Modules class
fix for neat_TSS intersection mode
added genes IDs into genome
* v1.3.2a
* v1.3.2pr
* v1.3.2rc0
* v1.3.2
* 1. main file split into parts
2. added different summary stats
3. started adding plotly
* 1. main file split into parts
2. added different summary stats
* custom labels
* plotly wip
* added seq_reader
* - major cleanup
- Moved to ArrowReaders.py
- Added PlotBase to Base.py
- Added more constructors to Metagene
- Added schema check for Metagene
* some fixes... more are coming 4 sure
* P_CG
and A LOT of documentation
* first merge to main
---
.github/workflows/publish.yaml | 16 +-
README.md | 200 ++-
docs/_binom.rst | 14 +
docs/_genome.rst | 41 +
docs/_metagene.rst | 14 +
docs/_plots.rst | 16 +
docs/_templates/autosummary/module.rst | 6 -
docs/_templates/class.rst | 25 +
docs/_templates/class_native.rst | 29 +
docs/_templates/method.rst | 4 +
docs/_templates/module.rst | 6 -
docs/conf.py | 24 +-
docs/images/boxplot/bp_ara_bradi_mpl.png | Bin 0 -> 11787 bytes
docs/images/boxplot/bp_ara_bradi_plotly.png | Bin 0 -> 24117 bytes
.../boxplot/bp_ara_bradi_plotly_nofilter.png | Bin 0 -> 26682 bytes
docs/images/boxplot/vp_ara_bradi_mpl.png | Bin 0 -> 18045 bytes
docs/images/boxplot/vp_ara_bradi_plotly.png | Bin 0 -> 33241 bytes
docs/images/heatmap/ara_bradi_mpl.png | Bin 0 -> 91972 bytes
docs/images/heatmap/ara_bradi_plotly.png | Bin 0 -> 100364 bytes
docs/images/heatmap/ara_mpl.png | Bin 0 -> 67312 bytes
docs/images/heatmap/ara_plotly.png | Bin 0 -> 119433 bytes
docs/images/lineplot/ara_NO_major_labels.png | Bin 0 -> 30140 bytes
docs/images/lineplot/ara_NO_minor_labels.png | Bin 0 -> 28073 bytes
docs/images/lineplot/ara_bradi_mpl.png | Bin 0 -> 41185 bytes
docs/images/lineplot/ara_bradi_plotly.png | Bin 0 -> 42775 bytes
docs/images/lineplot/ara_custom_label.png | Bin 0 -> 33508 bytes
docs/images/lineplot/ara_major_labels.png | Bin 0 -> 28482 bytes
docs/images/lineplot/ara_minor_labels.png | Bin 0 -> 30783 bytes
docs/images/lineplot/ara_multi_mpl.png | Bin 0 -> 41010 bytes
docs/images/lineplot/ara_multi_plotly.png | Bin 0 -> 82950 bytes
docs/images/lineplot/lp_ara_mpl.png | Bin 0 -> 33858 bytes
docs/index.rst | 22 +-
docs/markdowns/test.md | 128 ++
docs/requirements.txt | 2 +
pyproject.toml | 20 +-
src/bismarkplot/ArrowReaders.py | 122 ++
src/bismarkplot/Base.py | 226 +++
src/bismarkplot/Binom.py | 538 ++++++
src/bismarkplot/BismarkPlot.py | 1499 -----------------
src/bismarkplot/ChrLevels.py | 300 ++++
src/bismarkplot/Clusters.py | 294 ++++
src/bismarkplot/GenomeClass.py | 567 +++++++
src/bismarkplot/MetageneClasses.py | 1466 ++++++++++++++++
src/bismarkplot/Plots.py | 692 ++++++++
src/bismarkplot/SeqMapper.py | 460 +++++
src/bismarkplot/__init__.py | 8 +-
src/bismarkplot/console_chrs.py | 26 +-
src/bismarkplot/console_metagene.py | 78 +-
src/bismarkplot/utils.py | 110 ++
49 files changed, 5306 insertions(+), 1647 deletions(-)
create mode 100644 docs/_binom.rst
create mode 100644 docs/_genome.rst
create mode 100644 docs/_metagene.rst
create mode 100644 docs/_plots.rst
delete mode 100644 docs/_templates/autosummary/module.rst
create mode 100644 docs/_templates/class.rst
create mode 100644 docs/_templates/class_native.rst
create mode 100644 docs/_templates/method.rst
delete mode 100644 docs/_templates/module.rst
create mode 100644 docs/images/boxplot/bp_ara_bradi_mpl.png
create mode 100644 docs/images/boxplot/bp_ara_bradi_plotly.png
create mode 100644 docs/images/boxplot/bp_ara_bradi_plotly_nofilter.png
create mode 100644 docs/images/boxplot/vp_ara_bradi_mpl.png
create mode 100644 docs/images/boxplot/vp_ara_bradi_plotly.png
create mode 100644 docs/images/heatmap/ara_bradi_mpl.png
create mode 100644 docs/images/heatmap/ara_bradi_plotly.png
create mode 100644 docs/images/heatmap/ara_mpl.png
create mode 100644 docs/images/heatmap/ara_plotly.png
create mode 100644 docs/images/lineplot/ara_NO_major_labels.png
create mode 100644 docs/images/lineplot/ara_NO_minor_labels.png
create mode 100644 docs/images/lineplot/ara_bradi_mpl.png
create mode 100644 docs/images/lineplot/ara_bradi_plotly.png
create mode 100644 docs/images/lineplot/ara_custom_label.png
create mode 100644 docs/images/lineplot/ara_major_labels.png
create mode 100644 docs/images/lineplot/ara_minor_labels.png
create mode 100644 docs/images/lineplot/ara_multi_mpl.png
create mode 100644 docs/images/lineplot/ara_multi_plotly.png
create mode 100644 docs/images/lineplot/lp_ara_mpl.png
create mode 100644 docs/markdowns/test.md
create mode 100644 src/bismarkplot/ArrowReaders.py
create mode 100644 src/bismarkplot/Base.py
create mode 100644 src/bismarkplot/Binom.py
delete mode 100644 src/bismarkplot/BismarkPlot.py
create mode 100644 src/bismarkplot/ChrLevels.py
create mode 100644 src/bismarkplot/Clusters.py
create mode 100644 src/bismarkplot/GenomeClass.py
create mode 100644 src/bismarkplot/MetageneClasses.py
create mode 100644 src/bismarkplot/Plots.py
create mode 100644 src/bismarkplot/SeqMapper.py
create mode 100644 src/bismarkplot/utils.py
diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml
index e1f1d36..ce89bc4 100644
--- a/.github/workflows/publish.yaml
+++ b/.github/workflows/publish.yaml
@@ -1,8 +1,6 @@
name: Publish to PyPI and TestPyPI
-on:
- push:
- branches: [master] # branch to trigger deployment
+on: push
jobs:
build-n-publish:
@@ -24,12 +22,12 @@ jobs:
run: >-
python -m
build
- - name: Publish distribution 📦 to Test PyPI
- if: startsWith(github.ref, 'refs/tags')
- uses: pypa/gh-action-pypi-publish@release/v1
- with:
- password: ${{ secrets.TEST_PYPI_API_TOKEN }}
- repository-url: https://test.pypi.org/legacy/
+# - name: Publish distribution 📦 to Test PyPI
+# if: startsWith(github.ref, 'refs/tags')
+# uses: pypa/gh-action-pypi-publish@release/v1
+# with:
+# password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+# repository-url: https://test.pypi.org/legacy/
- name: Publish distribution 📦 to PyPI
if: startsWith(github.ref, 'refs/tags')
uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/README.md b/README.md
index 9bac9db..aa19e8d 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,6 @@
# BismarkPlot
-Comprehensive tool for visualizing genome-wide cytosine data.
+
+Analytical framework for BS-seq data comparison and visualization.
See the docs: https://shitohana.github.io/BismarkPlot
@@ -15,15 +16,14 @@ pip install bismarkplot
You can use ```bismarkplot``` either as python library or directly from console after installing it.
Console options:
-- *bismarkplot-metagene* - methylation density visualizing tool.
-- *bismarkplot-chrs* - chromosome methylation levels visualizing tool.
+- `bismarkplot-metagene` - methylation density visualizing tool.
+- `bismarkplot-chrs` - chromosome methylation levels visualizing tool.
### bismarkplot-metagene
```commandline
-usage: BismarkPlot. [-h] [-o OUT] [-g GENOME] [-r {gene,exon,tss,tes}] [-b BATCH] [-c CORES] [-f FLENGTH] [-u UWINDOWS] [-d DWINDOWS] [-m MLENGTH]
- [-w GWINDOWS] [--line] [--heatmap] [--box] [--violin] [-S SMOOTH] [-L LABELS [LABELS ...]] [-C CONFIDENCE] [-H H] [-V V] [--dpi DPI]
- [-F {png,pdf,svg}]
+usage: BismarkPlot. [-h] [-o NAME] [--dir DIR] [-g GENOME] [-r {gene,exon,tss,tes}] [-b BATCH] [-c CORES] [-f FLENGTH] [-u UWINDOWS] [-d DWINDOWS] [-m MLENGTH] [-w GWINDOWS] [--line] [--heatmap]
+ [--box] [--violin] [-S SMOOTH] [-L LABELS [LABELS ...]] [-C CONFIDENCE] [-H VRESOLUTION] [-V HRESOLUTION] [--dpi DPI] [-F {png,pdf,svg}]
filename [filename ...]
Metagene visualizing tool.
@@ -33,7 +33,8 @@ positional arguments:
optional arguments:
-h, --help show this help message and exit
- -o OUT, --out OUT output base name (default: /Users/shitohana/Desktop/PycharmProjects/BismarkPlot)
+ -o NAME, --out NAME output base name (default: plot)
+ --dir DIR output dir (default: /Users/shitohana/PycharmProjects/BismarkPlot_test)
-g GENOME, --genome GENOME
path to GFF genome file (default: None)
-r {gene,exon,tss,tes}, --region {gene,exon,tss,tes}
@@ -62,8 +63,8 @@ optional arguments:
labels for plots (default: None)
-C CONFIDENCE, --confidence CONFIDENCE
probability for confidence bands for line-plot. 0 if disabled (default: 0)
- -H H vertical resolution for heat-map (default: 100)
- -V V vertical resolution for heat-map (default: 100)
+ -H VRESOLUTION vertical resolution for heat-map (default: 100)
+ -V HRESOLUTION vertical resolution for heat-map (default: 100)
--dpi DPI dpi of output plot (default: 200)
-F {png,pdf,svg}, --format {png,pdf,svg}
format of output plots (default: pdf)
@@ -80,25 +81,27 @@ bismarkplot-metagene -g path/to/genome.gff -r gene -f 2000 -m 4000 -u 500 -d 50
### bismarkplot-chrs
```commandline
-usage: BismarkPlot [-h] [-o DIR] [-b N] [-c CORES] [-w N] [-m N] [-S FLOAT] [-F {png,pdf,svg}] path/to/txt [path/to/txt ...]
+usage: BismarkPlot [-h] [-o NAME] [-d DIR] [-b N] [-c CORES] [-w N] [-m N] [-S FLOAT] [-F {png,pdf,svg}] [--dpi DPI] path/to/txt
Chromosome methylation levels visualization.
positional arguments:
path/to/txt path to bismark methylation_extractor file
-options:
+optional arguments:
-h, --help show this help message and exit
- -o DIR, --out DIR output base name (default: current/path)
+ -o NAME, --out NAME output base name (default: plot)
+ -d DIR, --dir DIR output dir (default: /Users/shitohana/PycharmProjects/BismarkPlot_test)
-b N, --batch N number of rows to be read from bismark file by batch (default: 1000000)
-c CORES, --cores CORES
number of cores to use (default: None)
- -w N, --wlength N number of windows for genes (default: 100000)
+ -w N, --wlength N number of windows for chromosome (default: 100000)
-m N, --mlength N minimum chromosome length (default: 1000000)
-S FLOAT, --smooth FLOAT
windows for smoothing (0 - no smoothing, 1 - straight line (default: 50)
- -F {png,pdf,svg}, --format {png,pdf,svg}
+ -F {png,pdf,svg}, --fmt {png,pdf,svg}
format of output plots (default: pdf)
+ --dpi DPI dpi of output plot (default: 200)
```
Example:
@@ -120,36 +123,110 @@ Below we will show the basic BismarkPlot workflow.
### Single sample
```python
+import src.bismarkplot.Genome
import bismarkplot
+
# Firstly, we need to read the regions annotation (e.g. reference genome .gff)
-genome = bismarkplot.Genome.from_gff("path/to/genome.gff")
+genome = src.bismarkplot.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=4000, flank_length=2000)
# Now we need to calculate metagene data
-metagene = bismarkplot.Metagene.from_file(
- file = "path/to/CX_report.txt",
- genome=genes, # filtered regions
- upstream_windows = 500,
- gene_windows = 1000,
- downstream_windows = 500,
- batch_size= 10**7 # number of lines to be read simultaneously
+metagene = bismarkplot.Metagene.from_bismark(
+ file="path/to/CX_report.txt",
+ genome=genes, # filtered regions
+ up_windows=500,
+ body_windows=1000,
+ down_windows=500,
+ batch_size=10 ** 7 # number of lines to be read simultaneously
)
# Our metagene contains all methylation contexts and both strands, so we need to filter it (as in dplyr)
-filtered = metagene.filter(context = "CG", strand = "+")
+filtered = metagene.filter(context="CG", strand="+")
# We are ready to plot
-lp = filtered.line_plot() # line plot data
-lp.draw().savefig("path/to/lp.pdf") # matplotlib.Figure
+lp = filtered.line_plot() # line plot data
+lp.draw_mpl().savefig("path/to/lp.pdf") # matplotlib.Figure
hm = filtered.heat_map(ncol=200, nrow=200)
-hm.draw().savefig("path/to/hm.pdf") # matplotlib.Figure
+hm.draw_mpl().savefig("path/to/hm.pdf") # matplotlib.Figure
```
-Output:
+Output for _Brachypodium distachyon_:
- 
- 
+ 
+ 
+
+
+If metagene is not filtered by context, **all available contexts will be plotted**:
+
+```python
+filtered_by_strand = metagene.filter(strand == "+")
+lp = filtered_by_strand.line_plot()
+lp.draw_mpl()
+```
+
+Output for _Brachypodium distachyon_:
+
+
+ 
+
+
+**Confidence bands** can be visualized via setting the `confidence` parameter in `LinePlot.draw()`
+
+```python
+lp.draw_mpl(confidence=.95)
+```
+
+Output for _Brachypodium distachyon_:
+
+
+ 
+
+
+### Heat-map clusterisation
+
+Genes can be clustered to minimize distances between them before plotting heat-map. This can be useful for capturing
+overall methylation patterns in sample. _This operation is very time consuming. It is advised to set small number of
+windows (< 50)_.
+
+```python
+metagene = bismarkplot.Metagene.from_bismark(
+ file="path/to/CX_report.txt",
+ genome=genes, # filtered regions
+ up_windows=5, body_windows=10, down_windows=5,
+)
+clustered = metagene.clustering(
+ count_threshold=5, # Minimum counts per window
+ dist_method="euclidean", # See scipy.spatial.distance.pdist
+ clust_method="average" # See scipy.cluster.hierarchy.linkage
+)
+
+# Heatmap with optimized distances between genes will be drawn
+clustered.draw_mpl().savefig("path/to/clustered_hm.pdf")
+```
+Output for _Brachypodium distachyon_ - CHG
+
+
+ 
+
+
+### Genes dynamicTreeCut
+
+To shrink clustered heat-map and capture main patterns genes can be split into modules using
+[dynamicTreeCut algorithm](https://github.com/kylessmith/dynamicTreeCut/tree/master) by Peter Langfelder and Bin Zhang.
+Then genes can be plotted as heat-map as previous example:
+
+```python
+# Parameters are the same as for cutreeHybrid (see dynamicTreeCut)
+modules = clustered.modules(deepSplit=1)
+
+modules.draw_mpl().savefig("path/to/modules_hm.pdf")
+```
+
+Output for _Brachypodium distachyon_ - CHG
+
+
+ 
### Smoothing the line plot
@@ -158,12 +235,12 @@ Smoothing is very useful, when input signal is very weak (e.g. mammalian non-CpG
```python
# mouse CHG methylation example
-filtered = metagene.filter(context = "CHG", strand = "+")
-lp.draw(smooth = 0).savefig("path/to/lp.pdf") # no smooth
-lp.draw(smooth = 50).savefig("path/to/lp.pdf") # smoothed with window length = 50
+filtered = metagene.filter(context="CHG", strand="+")
+lp.draw_mpl(smooth=0).savefig("path/to/lp.pdf") # no smooth
+lp.draw_mpl(smooth=50).savefig("path/to/lp.pdf") # smoothed with window length = 50
```
-Output:
+Output for _Mus musculus_:
@@ -190,7 +267,7 @@ trimmed.violin_plot().savefig(...)
merged = filtered.merge()
```
-Output:
+Output for _Brachypodium distachyon_:
@@ -205,17 +282,19 @@ Output:
```python
# For analyzing samples with different reference genomes, we need to initialize several genomes instances
+import src.bismarkplot.Genome
+
genome_filenames = ["arabidopsis.gff", "brachypodium.gff", "cucumis.gff", "mus.gff"]
reports_filenames = ["arabidopsis.txt", "brachypodium.txt", "cucumis.txt", "mus.txt"]
genomes = [
- bismarkplot.Genome.from_gff(file).gene_body(...) for file in genome_filenames
+ src.bismarkplot.genome.Genome.from_gff(file).gene_body(...) for file in genome_filenames
]
# Now we read reports
metagenes = []
for report, genome in zip(reports_filenames, genomes):
- metagene = bismarkplot.Metagene(report, genome = genome, ...)
+ metagene = bismarkplot.Metagene(report, genome=genome, ...)
metagenes.append(metagene)
# Initialize MetageneFiles
@@ -240,26 +319,29 @@ Output:
Other genomic regions from .gff can be analyzed too with ```.exon``` or ```.near_tss/.near_tes``` option for ```bismarkplot.Genome```
```python
+import src.bismarkplot.Genome
+
exons = [
- bismarkplot.Genome.from_gff(file).exon(min_length=100) for file in genome_filenames
+ src.bismarkplot.genome.Genome.from_gff(file).exon(min_length=100) for file in genome_filenames
]
metagenes = []
for report, exon in zip(reports_filenames, exons):
- metagene = bismarkplot.Metagene(report, genome = exon,
- upstream_windows = 0, # !!!
- downstream_windows = 0, # !!!
+ metagene = bismarkplot.Metagene(report, genome=exon,
+ upstream_windows=0, # !!!
+ downstream_windows=0, # !!!
...)
metagenes.append(metagene)
# OR
tss = [
- bismarkplot.Genome.from_gff(file).near_tss(min_length = 2000, flank_length = 2000) for file in genome_filenames
+ src.bismarkplot.genome.Genome.from_gff(file).near_tss(min_length=2000, flank_length=2000) for file in
+ genome_filenames
]
metagenes = []
for report, t in zip(reports_filenames, tss):
- metagene = bismarkplot.Metagene(report, genome = t,
- upstream_windows = 1000,# same number of windows
- gene_windows = 1000, # same number of windows
- downstream_windows = 0, # !!!
+ metagene = bismarkplot.Metagene(report, genome=t,
+ upstream_windows=1000, # same number of windows
+ gene_windows=1000, # same number of windows
+ downstream_windows=0, # !!!
...)
metagenes.append(metagene)
```
@@ -281,29 +363,31 @@ TSS output:
BismarkPlot allows user to visualize chromosome methylation levels across full genome
```python
+import src.bismarkplot.ChrLevels
import bismarkplot
-chr = bismarkplot.ChrLevels.from_file(
+
+chr = src.bismarkplot.levels.ChrLevels.from_file(
"path/to/CX_report.txt",
- window_length=10**5, # window length in bp
- batch_size=10**7,
- chr_min_length = 10**6, # minimum chr length in bp
+ window_length=10 ** 5, # window length in bp
+ batch_size=10 ** 7,
+ chr_min_length=10 ** 6, # minimum chr length in bp
)
fig, axes = plt.subplots()
for context in ["CG", "CHG", "CHH"]:
- chr.filter(strand="+", context=context).draw(
- (fig, axes), # to plot contexts on same axes
- smooth=10, # window number for smoothing
- label=context # labels for lines
- )
+ chr.filter(strand="+", context=context).draw_mpl(
+ (fig, axes), # to plot contexts on same axes
+ smooth=10, # window number for smoothing
+ label=context # labels for lines
+ )
-fig.savefig(f"chrom.pdf", dpi = 200)
+fig.savefig(f"chrom.pdf", dpi=200)
```
-Output for Arabidopsis t.:
+Output for _Arabidopsis thaliana_:
-Output for Brachypodium d.:
+Output for _Brachypodium distachyon_:
-
\ No newline at end of file
+
diff --git a/docs/_binom.rst b/docs/_binom.rst
new file mode 100644
index 0000000..27b0d1a
--- /dev/null
+++ b/docs/_binom.rst
@@ -0,0 +1,14 @@
+Binomial
+========
+
+Methods for calculating P-value for cytosine residues or genomic regions.
+
+.. currentmodule:: bismarkplot
+
+.. autosummary::
+ :nosignatures:
+ :toctree: _Binom
+ :template: class.rst
+
+ RegionStat
+ BinomialData
\ No newline at end of file
diff --git a/docs/_genome.rst b/docs/_genome.rst
new file mode 100644
index 0000000..a30a7d2
--- /dev/null
+++ b/docs/_genome.rst
@@ -0,0 +1,41 @@
+Genome
+======
+
+Genome class
+
+.. currentmodule:: bismarkplot
+
+.. class:: Genome
+
+ .. rubric:: Methods
+
+ .. autosummary::
+ :nosignatures:
+ :toctree: _Genome/_method
+ :template: method.rst
+
+ ~Genome.all
+
+
+ ~Genome.cds
+
+
+ ~Genome.exon
+
+
+ ~Genome.from_custom
+
+
+ ~Genome.from_gff
+
+
+ ~Genome.gene_body
+
+
+ ~Genome.near_TES
+
+
+ ~Genome.near_TSS
+
+
+ ~Genome.other
diff --git a/docs/_metagene.rst b/docs/_metagene.rst
new file mode 100644
index 0000000..a24ccb1
--- /dev/null
+++ b/docs/_metagene.rst
@@ -0,0 +1,14 @@
+Metagene
+========
+
+Metagene calculation and plotting related methods.
+
+.. currentmodule:: bismarkplot
+
+.. autosummary::
+ :nosignatures:
+ :toctree: _Metagene
+ :template: class.rst
+
+ Metagene
+ MetageneFiles
diff --git a/docs/_plots.rst b/docs/_plots.rst
new file mode 100644
index 0000000..98e004a
--- /dev/null
+++ b/docs/_plots.rst
@@ -0,0 +1,16 @@
+Plots
+=====
+
+Reference for plotting classes.
+
+.. currentmodule:: bismarkplot
+
+.. autosummary::
+ :nosignatures:
+ :toctree: _Plots
+ :template: class.rst
+
+ LinePlot
+ LinePlotFiles
+ HeatMap
+ HeatMapFiles
\ No newline at end of file
diff --git a/docs/_templates/autosummary/module.rst b/docs/_templates/autosummary/module.rst
deleted file mode 100644
index 6c4a104..0000000
--- a/docs/_templates/autosummary/module.rst
+++ /dev/null
@@ -1,6 +0,0 @@
-{{ name }}
-{{ underline }}
-
-.. autoclass:: {{ fullname }}
- :special-members: __init__
- :members:
\ No newline at end of file
diff --git a/docs/_templates/class.rst b/docs/_templates/class.rst
new file mode 100644
index 0000000..d0b26c8
--- /dev/null
+++ b/docs/_templates/class.rst
@@ -0,0 +1,25 @@
+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. class:: {{ objname }}
+
+ {% block methods %}
+
+ {% if methods %}
+ .. rubric:: {{ _('Methods') }}
+
+ .. autosummary::
+ :nosignatures:
+ :toctree: _method
+ :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/_templates/class_native.rst b/docs/_templates/class_native.rst
new file mode 100644
index 0000000..0f7d6f3
--- /dev/null
+++ b/docs/_templates/class_native.rst
@@ -0,0 +1,29 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+
+ {% block methods %}
+ .. automethod:: __init__
+
+ {% if methods %}
+ .. rubric:: {{ _('Methods') }}
+
+ .. autosummary::
+ {% for item in methods %}
+ ~{{ name }}.{{ item }}
+ {%- endfor %}
+ {% endif %}
+ {% endblock %}
+
+ {% block attributes %}
+ {% if attributes %}
+ .. rubric:: {{ _('Attributes') }}
+
+ .. autosummary::
+ {% for item in attributes %}
+ ~{{ name }}.{{ item }}
+ {%- endfor %}
+ {% endif %}
+ {% endblock %}
diff --git a/docs/_templates/method.rst b/docs/_templates/method.rst
new file mode 100644
index 0000000..205c26f
--- /dev/null
+++ b/docs/_templates/method.rst
@@ -0,0 +1,4 @@
+{{ fullname }}
+{{ underline }}
+
+.. automethod:: {{ fullname }}
\ No newline at end of file
diff --git a/docs/_templates/module.rst b/docs/_templates/module.rst
deleted file mode 100644
index 6c4a104..0000000
--- a/docs/_templates/module.rst
+++ /dev/null
@@ -1,6 +0,0 @@
-{{ name }}
-{{ underline }}
-
-.. autoclass:: {{ fullname }}
- :special-members: __init__
- :members:
\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
index 1985e0d..d4ab189 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,29 +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'
+html_short_title = 'BismarkPlot Documentation'
+
+html_theme = 'sphinx_rtd_theme'
+html_show_sourcelink = False
-html_theme = 'sphinx_book_theme'
diff --git a/docs/images/boxplot/bp_ara_bradi_mpl.png b/docs/images/boxplot/bp_ara_bradi_mpl.png
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