import pathlib
import types
from typing import Any, List, Mapping, Optional, Sequence, Tuple, Union
import numpy as np
import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
from matplotlib import cm
from anndata import AnnData
from cellrank import logging as logg
from cellrank._utils import Lineage
from cellrank._utils._docs import d
from cellrank._utils._enum import DEFAULT_BACKEND, Backend_t
from cellrank._utils._parallelize import _get_n_cores
from cellrank._utils._utils import (
_check_collection,
_genesymbols,
_unique_order_preserving,
save_fig,
)
from cellrank.pl._utils import (
_callback_type,
_create_callbacks,
_create_models,
_fit_bulk,
_get_backend,
_input_model_type,
_return_model_type,
_time_range_type,
_trends_helper,
)
__all__ = ["gene_trends"]
[docs]
@d.dedent
@_genesymbols
def gene_trends(
adata: AnnData,
model: _input_model_type,
genes: Union[str, Sequence[str]],
time_key: str,
lineages: Optional[Union[str, Sequence[str]]] = None,
backward: bool = False,
data_key: str = "X",
time_range: Optional[Union[_time_range_type, List[_time_range_type]]] = None,
transpose: bool = False,
callback: _callback_type = None,
conf_int: Union[bool, float] = True,
same_plot: bool = False,
hide_cells: bool = False,
perc: Optional[Union[Tuple[float, float], Sequence[Tuple[float, float]]]] = None,
lineage_cmap: Optional[matplotlib.colors.ListedColormap] = None,
fate_prob_cmap: matplotlib.colors.ListedColormap = cm.viridis,
cell_color: Optional[str] = None,
cell_alpha: float = 0.6,
lineage_alpha: float = 0.2,
size: float = 15,
lw: float = 2,
cbar: bool = True,
margins: float = 0.015,
sharex: Optional[Union[str, bool]] = None,
sharey: Optional[Union[str, bool]] = None,
gene_as_title: Optional[bool] = None,
legend_loc: Optional[str] = "best",
obs_legend_loc: Optional[str] = "best",
ncols: int = 2,
suptitle: Optional[str] = None,
return_models: bool = False,
n_jobs: Optional[int] = 1,
backend: Backend_t = DEFAULT_BACKEND,
show_progress_bar: bool = True,
figsize: Optional[Tuple[float, float]] = None,
dpi: Optional[int] = None,
save: Optional[Union[str, pathlib.Path]] = None,
return_figure: bool = False,
plot_kwargs: Mapping[str, Any] = types.MappingProxyType({}),
**kwargs: Any,
) -> Optional[_return_model_type]:
"""Plot gene expression trends along lineages.
.. seealso::
- See :doc:`../../../notebooks/tutorials/estimators/800_gene_trends` on how to
visualize the gene trends.
Each lineage is defined via its lineage weights. This function accepts any model based off
:class:`~cellrank.models.BaseModel` to fit gene expression, where we take the lineage weights
into account in the loss function.
Parameters
----------
%(adata)s
%(model)s
%(genes)s
time_key
Key in :attr:`~anndata.AnnData.obs` where the pseudotime is stored.
lineages
Names of the lineages to plot. If :obj:`None`, plot all lineages.
%(backward)s
data_key
Key in :attr:`~anndata.AnnData.layers` or ``'X'`` for :attr:`~anndata.AnnData.X` where the data is stored.
%(time_range)s
This can also be specified on per-lineage basis.
%(gene_symbols)s
transpose
If ``same_plot = True``, group the trends by ``lineages`` instead of ``genes``.
This forces ``hide_cells = True``.
If ``same_plot = False``, show ``lineages`` in rows and ``genes`` in columns.
%(model_callback)s
conf_int
Whether to compute and show confidence interval. If the ``model`` is :class:`~cellrank.models.GAMR`,
it can also specify the confidence level, the default is :math:`0.95`.
same_plot
Whether to plot all lineages for each gene in the same plot.
hide_cells
If :obj:`True`, hide all cells.
perc
Percentile for colors. Valid values are in :math:`[0, 100]`.
This can improve visualization. Can be specified individually for each lineage.
lineage_cmap
Categorical colormap to use when coloring in the lineages. If :obj:`None` and ``same_plot = True``,
use the corresponding colors in :attr:`~anndata.AnnData.uns`, otherwise use ``'black'``.
fate_prob_cmap
Continuous colormap to use when visualizing the fate probabilities for each lineage.
Only used when ``same_plot = False``.
cell_color
Key in :attr:`~anndata.AnnData.obs` or :attr:`~anndata.AnnData.var_names` used for coloring the cells.
cell_alpha
Alpha channel for cells.
lineage_alpha
Alpha channel for lineage confidence intervals.
size
Size of the points.
lw
Line width of the smoothed values.
cbar
Whether to show colorbar. Always shown when percentiles for lineages differ.
Only used when ``same_plot = False``.
margins
Margins around the plot.
sharex
Whether to share x-axis. Valid options are ``'row'``, ``'col'`` or ``'none'``.
sharey
Whether to share y-axis. Valid options are ``'row'`, ``'col'`` or ``'none'``.
gene_as_title
Whether to show gene names as titles instead on y-axis.
legend_loc
Location of the legend displaying lineages. Only used when ``same_plot = True``.
obs_legend_loc
Location of the legend when ``cell_color`` corresponds to a categorical variable.
ncols
Number of columns of the plot when plotting multiple genes. Only used when ``same_plot = True``.
suptitle
Suptitle of the figure.
return_figure
Whether to return the figure object.
%(return_models)s
%(parallel)s
%(plotting)s
plot_kwargs
Keyword arguments for the :meth:`~cellrank.models.BaseModel.plot`.
kwargs
Keyword arguments for :meth:`~cellrank.models.BaseModel.prepare`.
Returns
-------
%(plots_or_returns_models)s
"""
if isinstance(genes, str):
genes = [genes]
genes = _unique_order_preserving(genes)
_check_collection(
adata,
genes,
"obs" if data_key == "obs" else "var_names",
use_raw=kwargs.get("use_raw", False),
)
probs = Lineage.from_adata(adata, backward=backward)
if lineages is None:
lineages = probs.names
elif isinstance(lineages, str):
lineages = [lineages]
elif all(ln is None for ln in lineages): # no lineage, all the weights are 1
lineages = [None]
cbar = False
logg.debug("All lineages are `None`, setting the weights to `1`")
lineages = _unique_order_preserving(lineages)
if isinstance(time_range, (tuple, float, int, type(None))):
time_range = [time_range] * len(lineages)
elif len(time_range) != len(lineages):
raise ValueError(f"Expected time ranges to be of length `{len(lineages)}`, found `{len(time_range)}`.")
kwargs["time_key"] = time_key
kwargs["data_key"] = data_key
kwargs["backward"] = backward
kwargs["conf_int"] = conf_int # prepare doesnt take or need this
models = _create_models(model, genes, lineages)
all_models, models, genes, lineages = _fit_bulk(
models,
_create_callbacks(adata, callback, genes, lineages, **kwargs),
genes,
lineages,
time_range,
return_models=True,
filter_all_failed=False,
parallel_kwargs={
"show_progress_bar": show_progress_bar,
"n_jobs": _get_n_cores(n_jobs, len(genes)),
"backend": _get_backend(models, backend),
},
**kwargs,
)
lineages = sorted(lineages)
probs = probs[lineages]
if lineage_cmap is None and not transpose:
lineage_cmap = probs.colors
plot_kwargs = dict(plot_kwargs)
plot_kwargs["obs_legend_loc"] = obs_legend_loc
if transpose:
all_models = pd.DataFrame(all_models).T.to_dict()
models = pd.DataFrame(models).T.to_dict()
genes, lineages = lineages, genes
hide_cells = same_plot or hide_cells
else:
# information overload otherwise
plot_kwargs["lineage_probability"] = False
plot_kwargs["lineage_probability_conf_int"] = False
tmp = pd.DataFrame(models).T.astype(bool)
start_rows = np.argmax(tmp.values, axis=0)
end_rows = tmp.shape[0] - np.argmax(tmp[::-1].values, axis=0) - 1
if same_plot:
gene_as_title = True if gene_as_title is None else gene_as_title
sharex = "all" if sharex is None else sharex
if sharey is None:
sharey = "row" if plot_kwargs.get("lineage_probability", False) else "none"
ncols = len(genes) if ncols >= len(genes) else ncols
nrows = int(np.ceil(len(genes) / ncols))
else:
gene_as_title = False if gene_as_title is None else gene_as_title
sharex = "col" if sharex is None else sharex
if sharey is None:
sharey = "row" if not hide_cells or plot_kwargs.get("lineage_probability", False) else "none"
nrows = len(genes)
ncols = len(lineages)
plot_kwargs = dict(plot_kwargs)
if plot_kwargs.get("xlabel", None) is None:
plot_kwargs["xlabel"] = time_key
fig, axes = plt.subplots(
nrows=nrows,
ncols=ncols,
sharex=sharex,
sharey=sharey,
figsize=(6 * ncols, 4 * nrows) if figsize is None else figsize,
tight_layout=True,
dpi=dpi,
)
axes = np.reshape(axes, (nrows, ncols))
cnt = 0
plot_kwargs["obs_legend_loc"] = None if same_plot else obs_legend_loc
logg.info("Plotting trends")
for row in range(len(axes)):
for col in range(len(axes[row])):
if cnt >= len(genes):
break
gene = genes[cnt]
if same_plot and plot_kwargs.get("lineage_probability", False) and transpose:
lpc = probs[gene].colors[0]
else:
lpc = None
if same_plot:
plot_kwargs["obs_legend_loc"] = obs_legend_loc if row == 0 and col == len(axes[0]) - 1 else None
_trends_helper(
models,
gene=gene,
lineage_names=lineages,
transpose=transpose,
same_plot=same_plot,
hide_cells=hide_cells,
perc=perc,
lineage_cmap=lineage_cmap,
fate_prob_cmap=fate_prob_cmap,
lineage_probability_color=lpc,
cell_color=cell_color,
alpha=cell_alpha,
lineage_alpha=lineage_alpha,
size=size,
lw=lw,
cbar=cbar,
margins=margins,
sharey=sharey,
gene_as_title=gene_as_title,
legend_loc=legend_loc,
figsize=figsize,
fig=fig,
axes=axes[row, col] if same_plot else axes[cnt],
show_ylabel=col == 0,
show_lineage=same_plot or (cnt == start_rows),
show_xticks_and_label=((row + 1) * ncols + col >= len(genes)) if same_plot else (cnt == end_rows),
**plot_kwargs,
)
cnt += 1 # plot legend on the 1st plot
if not same_plot:
plot_kwargs["obs_legend_loc"] = None
if same_plot and (col != ncols):
for ax in np.ravel(axes)[cnt:]:
ax.remove()
fig.suptitle(suptitle, y=1.05)
if return_figure:
return fig
if save is not None:
save_fig(fig, save)
if return_models:
return all_models