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Implement pl.plot_connectivity() #652

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Feb 26, 2024
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Implement pl.plot_connectivity() #652

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774fd99
create plot_connectivity func
Sichao25 Jan 23, 2024
741fb6b
Merge branch 'master' into dependency
Sichao25 Feb 21, 2024
3e35185
enable str input
Sichao25 Feb 21, 2024
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3 changes: 2 additions & 1 deletion dynamo/plot/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@

from .cell_cycle import cell_cycle_scores
from .clustering import infomap, leiden, louvain, streamline_clusters
from .connectivity import nneighbors
from .connectivity import nneighbors, plot_connectivity
from .dimension_reduction import pca, trimap, tsne, umap
from .dynamics import dynamics, phase_portraits
from .ezplots import (
Expand Down Expand Up @@ -105,6 +105,7 @@
"umap",
"trimap",
"nneighbors",
"plot_connectivity",
"cell_wise_vectors",
"cell_wise_vectors_3d",
"grid_vectors",
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258 changes: 258 additions & 0 deletions dynamo/plot/connectivity.py
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Expand Up @@ -28,6 +28,7 @@
from anndata import AnnData
from matplotlib.axes import Axes
from matplotlib.figure import Figure
from scipy.sparse import csc_matrix, csr_matrix, issparse

from ..configuration import _themes
from ..docrep import DocstringProcessor
Expand Down Expand Up @@ -564,6 +565,263 @@ def nneighbors(



def plot_connectivity(
adata: AnnData,
graph: Union[csr_matrix, csc_matrix, np.ndarray],
x: int = 0,
y: int = 1,
color: Union[str, List[str]] = ["ntr"],
basis: Union[str, List[str]] = ["umap"],
layer: Union[str, List[str]] = ["X"],
highlights: Optional[list] = None,
ncols: int = 1,
edge_bundling: Optional[Literal["hammer"]] = None,
edge_cmap: str = "gray_r",
show_points: bool = True,
labels: Optional[list] = None,
values: Optional[list] = None,
theme: Optional[
Literal[
"blue",
"red",
"green",
"inferno",
"fire",
"viridis",
"darkblue",
"darkgreen",
"darkred",
]
] = None,
cmap: str = "Blues",
color_key: Union[dict, list, None] = None,
color_key_cmap: str = "Spectral",
background: str = "black",
figsize: tuple = (6, 4),
ax: Optional[Axes] = None,
save_show_or_return: Literal["save", "show", "return"] = "return",
save_kwargs: dict = {},
) -> Optional[Figure]:
"""Plot the connectivity graph.

A connectivity graph can be one of the followings:
1. nneighbors: kNN graph constructed from umap/scKDTree/annoy, etc.
2. mutual kNN shared between spliced or unspliced layer
3. principal graph that learnt from DDRTree, L1graph or other principal graph algorithms
4. regulatory network learnt from Scribe
5. spatial kNN graph
6. others

Args:
adata: an Annodata object that include the umap embedding and simplicial graph.
graph: the matrix representing the connectivity relationship. For example `adata.obsp["connectivities"]` or
`adata.uns["neighbors"]["connectivities"]`. Notice that the matrix should have the same size as the data.
x: the first component of the embedding. Defaults to 0.
y: the second component of the embedding. Defaults to 1.
color: gene name(s) or cell annotation column(s) used for coloring the graph. Defaults to ["ntr"].
basis: the low dimensional embedding to be used to visualize the cell. Defaults to ["umap"].
layer: the layers of data representing the gene expression level. Defaults to ["X"].
highlights: the list that cells will be restricted to. Defaults to None.
ncols: the number of columns to be plotted. Defaults to 1.
edge_bundling: the edge bundling method to use. Currently supported are None or 'hammer'. See the datashader
docs on graph visualization for more details. Defaults to None.
edge_cmap: the name of a matplotlib colormap to use for shading/coloring the edges of the connectivity graph.
Note that the `theme`, if specified, will override this. Defaults to "gray_r".
show_points: whether to display the points over top of the edge connectivity. Further options allow for
coloring/shading the points accordingly. Defaults to True.
labels: an array of labels (assumed integer or categorical), one for each data sample. This will be used for
coloring the points in the plot according to their label. Note that this option is mutually exclusive to the
`values` option. Defaults to None.
values: an array of values (assumed float or continuous), one for each sample. This will be used for coloring
the points in the plot according to a colorscale associated to the total range of values. Note that this
option is mutually exclusive to the `labels` option. Defaults to None.
theme: a color theme to use for plotting. A small set of predefined themes are provided which have relatively
good aesthetics. Available themes are:
* 'blue'
* 'red'
* 'green'
* 'inferno'
* 'fire'
* 'viridis'
* 'darkblue'
* 'darkred'
* 'darkgreen'.
Defaults to None.
cmap: the name of a matplotlib colormap to use for coloring or shading points. If no labels or values are passed
this will be used for shading points according to density (largely only of relevance for very large
datasets). If values are passed this will be used for shading according the value. Note that if theme is
passed then this value will be overridden by the corresponding option of the theme. Defaults to "Blues".
color_key: a way to assign colors to categoricals. This can either be an explicit dict mapping labels to colors
(as strings of form '#RRGGBB'), or an array like object providing one color for each distinct category being
provided in `labels`. Either way this mapping will be used to color points according to the label. Note that
if theme is passed then this value will be overridden by the corresponding option of the theme. Defaults to
None.
color_key_cmap: the name of a matplotlib colormap to use for categorical coloring. If an explicit `color_key` is
not given a color mapping for categories can be generated from the label list and selecting a matching list
of colors from the given colormap. Note that if theme is passed then this value will be overridden by the
corresponding option of the theme. Defaults to "Spectral".
background: the color of the background. Usually this will be either 'white' or 'black', but any color name will
work. Ideally one wants to match this appropriately to the colors being used for points etc. This is one of
the things that themes handle for you. Note that if theme is passed then this value will be overridden by
the corresponding option of the theme. Defaults to "black".
figsize: the desired size of the figure. Defaults to (6, 4).
ax: the axis on which the subplot would be shown. If set to be `None`, a new axis would be created. Defaults to
None.
save_show_or_return: whether to save, show or return the figure. Defaults to "return".
save_kwargs: a dictionary that will be passed to the save_show_ret function. By default, it is an empty dictionary
and the save_show_ret function will use the
{
"path": None,
"prefix": 'connectivity_base',
"dpi": None,
"ext": 'pdf',
"transparent": True,
"close": True,
"verbose": True
}
as its parameters. Otherwise, you can provide a dictionary that properly modify those keys according to your
needs. Defaults to {}.

Raises:
TypeError: wrong type of `x` and `y`.

Returns:
The matplotlib axis with the plotted connectivity graph by default. If `save_show_or_return` is set to be
`"show"` or `"save"`, nothing would be returned.
"""

import matplotlib.pyplot as plt
import seaborn as sns

if type(x) is not int or type(y) is not int:
raise TypeError("x, y have to be integers (components in the a particular embedding {}) ".format(basis))

basis = [basis] if isinstance(basis, str) else basis
color = [color] if isinstance(color, str) else color
layer = [layer] if isinstance(layer, str) else layer

n_c, n_l, n_b = (
0 if color is None else len(color),
0 if layer is None else len(layer),
0 if basis is None else len(basis),
)

check_and_recompute_neighbors(adata, result_prefix="")
coo_graph = graph.tocoo() if issparse(graph) else csr_matrix(graph).tocoo()

edge_df = pd.DataFrame(
np.vstack([coo_graph.row, coo_graph.col, coo_graph.data]).T,
columns=("source", "target", "weight"),
)
edge_df["source"] = edge_df.source.astype(np.int32)
edge_df["target"] = edge_df.target.astype(np.int32)

total_panels, ncols = n_c * n_l * n_b, min(n_c, ncols)
nrow, ncol = int(np.ceil(total_panels / ncols)), ncols
if figsize is None:
figsize = plt.rcParams["figsize"]

font_color = _select_font_color(background)
if background == "black":
# https://github.com/matplotlib/matplotlib/blob/master/lib/matplotlib/mpl-data/stylelib/dark_background.mplstyle
sns.set(
rc={
"axes.facecolor": background,
"axes.edgecolor": background,
"figure.facecolor": background,
"figure.edgecolor": background,
"axes.grid": False,
"ytick.color": font_color,
"xtick.color": font_color,
"axes.labelcolor": font_color,
"axes.edgecolor": font_color,
"savefig.facecolor": "k",
"savefig.edgecolor": "k",
"grid.color": font_color,
"text.color": font_color,
"lines.color": font_color,
"patch.edgecolor": font_color,
"figure.edgecolor": font_color,
}
)
else:
sns.set(
rc={
"axes.facecolor": background,
"figure.facecolor": background,
"axes.grid": False,
}
)

if total_panels > 1:
g = plt.figure(None, (figsize[0] * ncol, figsize[1] * nrow), facecolor=background)
gs = plt.GridSpec(nrow, ncol, wspace=0.12)

i = 0
for cur_b in basis:
for cur_l in layer:
prefix = cur_l + "_"
if prefix + cur_b in adata.obsm.keys():
x_, y_ = (
adata.obsm[prefix + cur_b][:, int(x)],
adata.obsm[prefix + cur_b][:, int(y)],
)
else:
continue
for cur_c in color:
_color = adata.obs_vector(cur_c, layer=cur_l)
is_not_continous = _color.dtype.name == "category"
if is_not_continous:
labels = _color
if theme is None:
theme = "glasbey_dark"
else:
values = _color
if theme is None:
theme = "inferno" if cur_l != "velocity" else "div_blue_red"

if total_panels > 1:
ax = plt.subplot(gs[i])
i += 1

# if highligts is a list of lists - each list is relate to each color element
if highlights is not None:
if is_list_of_lists(highlights):
_highlights = highlights[color.index(cur_c)]
_highlights = _highlights if all([i in _color for i in _highlights]) else None
else:
_highlights = highlights if all([i in _color for i in highlights]) else None
else:
_highlights = None

ax = connectivity_base(
x_,
y_,
edge_df,
_highlights,
edge_bundling,
edge_cmap,
show_points,
labels,
values,
theme,
cmap,
color_key,
color_key_cmap,
background,
figsize,
ax,
)

ax.set_xlabel(
cur_b + "_1",
)
ax.set_ylabel(cur_b + "_2")
ax.set_title(cur_c)

return save_show_ret("nneighbors", save_show_or_return, save_kwargs, plt.gcf())


def pgraph():
"""Plot principal graph of cells that learnt from graph embedding algorithms.

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