Skip to content

Commit

Permalink
Merge pull request #1 from YosefLab/tree-plot
Browse files Browse the repository at this point in the history 
tree annotation
  • Loading branch information
@colganwi
colganwi authored May 15, 2024
2 parents 574d096 + 68f3cee commit 138835a
Show file tree
Hide file tree
Showing 19 changed files with 851 additions and 371 deletions.
23 changes: 3 additions & 20 deletions docs/api.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,28 +2,8 @@

## Preprocessing

```{eval-rst}
.. module:: pycea.pp
.. currentmodule:: pycea
.. autosummary::
:toctree: generated
pp.basic_preproc
```

## Tools

```{eval-rst}
.. module:: pycea.tl
.. currentmodule:: pycea
.. autosummary::
:toctree: generated
tl.basic_tool
```

## Plotting

```{eval-rst}
Expand All @@ -33,5 +13,8 @@
.. autosummary::
:toctree: generated
pl.tree
pl.branches
pl.nodes
pl.annotation
```
8 changes: 7 additions & 1 deletion docs/conf.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -91,10 +91,16 @@
}

intersphinx_mapping = {
"python": ("https://docs.python.org/3", None),
"anndata": ("https://anndata.readthedocs.io/en/stable/", None),
"cycler": ("https://matplotlib.org/cycler/", None),
"matplotlib": ("https://matplotlib.org/stable/", None),
"numpy": ("https://numpy.org/doc/stable/", None),
"networkx": ("https://networkx.org/documentation/stable/", None),
"pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
"python": ("https://docs.python.org/3", None),
"scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
"scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
"squidpy": ("https://squidpy.readthedocs.io/en/stable/", None),
"treedata": ("https://treedata.readthedocs.io/en/stable/", None),
}

Expand Down
129 changes: 1 addition & 128 deletions docs/notebooks/example.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,134 +12,7 @@
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"from anndata import AnnData\n",
"import pandas as pd\n",
"import pycea"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"adata = AnnData(np.random.normal(size=(20, 10)))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"With myst it is possible to link in the text cell of a notebook such as this one the documentation of a function or a class.\n",
"\n",
"Let's take as an example the function {func}`pycea.pp.basic_preproc`. \n",
"You can see that by clicking on the text, the link redirects to the API documentation of the function. \n",
"Check the raw markdown of this cell to understand how this is specified.\n",
"\n",
"This works also for any package listed by `intersphinx`. Go to `docs/conf.py` and look for the `intersphinx_mapping` variable. \n",
"There, you will see a list of packages (that this package is dependent on) for which this functionality is supported. \n",
"\n",
"For instance, we can link to the class {class}`anndata.AnnData`, to the attribute {attr}`anndata.AnnData.obs` or the method {meth}`anndata.AnnData.write`.\n",
"\n",
"Again, check the raw markdown of this cell to see how each of these links are specified.\n",
"\n",
"You can read more about this in the [intersphinx page](https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html) and the [myst page](https://myst-parser.readthedocs.io/en/v0.15.1/syntax/syntax.html#roles-an-in-line-extension-point)."
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Implement a preprocessing function here."
]
},
{
"data": {
"text/plain": [
"0"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pycea.pp.basic_preproc(adata)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>A</th>\n",
" <th>B</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>a</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>b</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>c</td>\n",
" <td>3</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" A B\n",
"0 a 1\n",
"1 b 2\n",
"2 c 3"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pd.DataFrame().assign(A=[\"a\", \"b\", \"c\"], B=[1, 2, 3])"
]
"source": []
}
],
"metadata": {
Expand Down
24 changes: 0 additions & 24 deletions src/pycea/_utils.py
View file

This file was deleted.

2 changes: 1 addition & 1 deletion src/pycea/pl/__init__.py
View file
Original file line number Diff line number Diff line change
@@ -1 +1 @@
from .tree import branches
from .plot_tree import annotation, branches, nodes, tree
22 changes: 20 additions & 2 deletions src/pycea/pl/_docs.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,27 @@

from __future__ import annotations

from textwrap import dedent


def _doc_params(**kwds):
r"""Docstrings should start with ``\\`` in the first line for proper formatting"""

def dec(obj):
obj.__orig_doc__ = obj.__doc__
obj.__doc__ = dedent(obj.__doc__).format_map(kwds)
return obj

return dec


doc_common_plot_args = """\
color_map
cmap
Color map to use for continous variables. Can be a name or a
:class:`~matplotlib.colors.Colormap` instance (e.g. `"magma`", `"viridis"`
or `mpl.cm.cividis`), see :func:`~matplotlib.cm.get_cmap`.
If `None`, the value of `mpl.rcParams["image.cmap"]` is used.
The default `color_map` can be set using :func:`~scanpy.set_figure_params`.
The default `cmap` can be set using :func:`~scanpy.set_figure_params`.
palette
Colors to use for plotting categorical annotation groups.
The palette can be a valid :class:`~matplotlib.colors.ListedColormap` name
Expand All @@ -18,6 +32,10 @@
If `None`, `mpl.rcParams["axes.prop_cycle"]` is used unless the categorical
variable already has colors stored in `tdata.uns["{var}_colors"]`.
If provided, values of `tdata.uns["{var}_colors"]` will be set.
vmax
The maximum value for the colormap.
vmin
The minimum value for the colormap.
ax
A matplotlib axes object. If `None`, a new figure and axes will be created.
"""
60 changes: 58 additions & 2 deletions src/pycea/pl/_utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
import numpy as np
from scanpy.plotting import palettes

from pycea._utils import get_root
from pycea.utils import get_root


def layout_tree(
Expand Down Expand Up @@ -62,7 +62,7 @@ def layout_tree(
node_coords = {}
for node in nx.dfs_postorder_nodes(tree, root):
if tree.out_degree(node) == 0:
lon = (i / n_leaves) * 2 * np.pi
lon = (i / (n_leaves)) * 2 * np.pi # + 2 * np.pi / n_leaves
if extend_branches:
node_coords[node] = (max_depth, lon)
else:
Expand Down Expand Up @@ -175,3 +175,59 @@ def _get_categorical_colors(tdata, key, data, palette=None):
# store colors in tdata
tdata.uns[key + "_colors"] = colors_list
return dict(zip(categories, colors_list))


def _get_categorical_markers(tdata, key, data, markers=None):
"""Get categorical markers for plotting."""
default_markers = ["o", "s", "D", "^", "v", "<", ">", "p", "P", "*", "h", "H", "X"]
# Ensure data is a category
if not data.dtype.name == "category":
data = data.astype("category")
categories = data.cat.categories
# Use default markers if no markers are provided
if markers is None:
markers_list = tdata.uns.get(key + "_markers", None)
if markers_list is None or len(markers_list) > len(categories):
markers_list = default_markers[: len(categories)]
# Use provided markers
else:
if isinstance(markers, cabc.Mapping):
markers_list = [markers[k] for k in categories]
else:
if not isinstance(markers, cabc.Sequence):
raise ValueError("Please check that the value of 'markers' is a valid " "list of marker names.")
if len(markers) < len(categories):
warnings.warn(
"Length of markers is smaller than the number of "
f"categories (markers length: {len(markers)}, "
f"categories length: {len(categories)}. "
"Some categories will have the same marker.",
stacklevel=2,
)
markers_list = markers * (len(categories) // len(markers) + 1)
else:
markers_list = markers[: len(categories)]
# store markers in tdata
tdata.uns[key + "_markers"] = markers_list
return dict(zip(categories, markers_list))


def _series_to_rgb_array(series, colors, vmin=None, vmax=None, na_color="#808080"):
"""Converts a pandas Series to an N x 3 numpy array based using a color map."""
if isinstance(colors, dict):
# Map using the dictionary
color_series = series.map(colors)
color_series[series.isna()] = na_color
rgb_array = np.array([mcolors.to_rgb(color) for color in color_series])
elif isinstance(colors, mcolors.ListedColormap):
# Normalize and map values if cmap is a ListedColormap
if vmin is not None and vmax is not None:
norm = mcolors.Normalize(vmin, vmax)
colors.set_bad(na_color)
color_series = colors(norm(series))
rgb_array = np.vstack(color_series[:, :3])
else:
raise ValueError("vmin and vmax must be specified when using a ListedColormap.")
else:
raise ValueError("cmap must be either a dictionary or a ListedColormap.")
return rgb_array
Loading

0 comments on commit 138835a

Please sign in to comment.