def _sanitize_anndata(adata: AnnData) -> None:
"""Sanitization and sanity checks on TCR-anndata object.
Should be executed by every read_xxx function"""
assert (len(adata.X.shape) == 2
), "X needs to have dimensions, otherwise concat doesn't work. "
# This should always be a categorical with True / False
has_tcr_mask = _is_true(adata.obs["has_tcr"])
adata.obs["has_tcr"] = ["True" if x else "False" for x in has_tcr_mask]
adata._sanitize()
def _sanitize_anndata(adata: AnnData) -> None:
"""Sanitization and sanity checks on IR-anndata object.
Should be executed by every read_xxx function"""
assert (len(adata.X.shape) == 2
), "X needs to have dimensions, otherwise concat doesn't work. "
CATEGORICAL_COLS = ("locus", "v_gene", "d_gene", "j_gene", "c_gene",
"multichain")
# Sanitize has_ir column into categorical
# This should always be a categorical with True / False
has_ir_mask = _is_true(adata.obs["has_ir"])
adata.obs["has_ir"] = pd.Categorical(
["True" if x else "False" for x in has_ir_mask])
# Turn other columns into categorical
for col in adata.obs.columns:
if col.endswith(CATEGORICAL_COLS):
adata.obs[col] = pd.Categorical(adata.obs[col])
adata._sanitize()
def adata_cdr3():
obs = pd.DataFrame(
[
[
"cell1",
"AAA",
"AHA",
"KKY",
"KKK",
"GCGGCGGCG",
"TRA",
"TRB",
"TRA",
"TRB",
],
[
"cell2",
"AHA",
"nan",
"KK",
"KKK",
"GCGAUGGCG",
"TRA",
"TRB",
"TRA",
"TRB",
],
# This row has no chains, but "has_ir" = True. That can happen if
# the user does not filter the data.
[
"cell3",
"nan",
"nan",
"nan",
"nan",
"nan",
"nan",
"nan",
"nan",
"nan",
],
[
"cell4",
"AAA",
"AAA",
"LLL",
"AAA",
"GCUGCUGCU",
"TRA",
"TRB",
"TRA",
"TRB",
],
[
"cell5",
"AAA",
"nan",
"LLL",
"nan",
"nan",
"nan",
"TRB",
"TRA",
"nan",
],
],
columns=[
"cell_id",
"IR_VJ_1_junction_aa",
"IR_VJ_2_junction_aa",
"IR_VDJ_1_junction_aa",
"IR_VDJ_2_junction_aa",
"IR_VJ_1_junction",
"IR_VJ_1_locus",
"IR_VJ_2_locus",
"IR_VDJ_1_locus",
"IR_VDJ_2_locus",
],
).set_index("cell_id")
obs["has_ir"] = "True"
adata = AnnData(obs=obs)
adata._sanitize()
adata.uns["scirpy_version"] = "0.7"
return adata
def test_slicing_remove_unused_categories():
adata = AnnData(np.array([[1, 2], [3, 4], [5, 6], [7, 8]]),
dict(k=["a", "a", "b", "b"]))
adata._sanitize()
assert adata[2:4].obs["k"].cat.categories.tolist() == ["b"]
def test_slicing_remove_unused_categories():
adata = AnnData(np.array([[1, 2], [3, 4], [5, 6], [7, 8]]),
dict(k=['a', 'a', 'b', 'b']))
adata._sanitize()
assert adata[3:5].obs['k'].cat.categories.tolist() == ['b']
def embedding(
adata: AnnData,
basis: str,
*,
color: Union[str, Sequence[str], None] = None,
panel_size: Tuple[float, float] = (4, 4),
palette: Union[str, Cycler, Sequence[str], Sequence[Cycler], None] = None,
legend_loc: str = "right margin",
ax: Optional[Union[plt.Axes, Sequence[plt.Axes]]] = None,
ncols: int = 3,
show: Optional[bool] = False,
hspace: float = 0.25,
wspace: float = None,
**kwargs,
) -> Union[None, Sequence[plt.Axes]]:
"""A customized wrapper to the :func:`scanpy.pl.embedding` function.
The differences to the scanpy embedding function are:
* allows to specify a `panel_size`
* Allows to specify a different `basis`, `legend_loc` and `palette`
for each panel. The number of panels is defined by the `color` parameter.
* Use a patched version for adding "on data" labels. The original
raises a flood of warnings when coords are `nan`.
* For columns with many categories, cycles through colors
instead of reverting to grey
* allows to specify axes, even if multiple colors are set.
Parameters
----------
adata
annotated data matrix
basis
embedding to plot.
Get the coordinates from the "X_{basis}" key in `adata.obsm`.
This can be a list of the same length as `color` to specify
different bases for each panel.
color
Keys for annotations of observations/cells or variables/genes, e.g.,
`'ann1'` or `['ann1', 'ann2']`.
panel_size
Size tuple (`width`, `height`) of a single panel in inches
palette
Colors to use for plotting categorical annotation groups.
The palette can be a valid :class:`~matplotlib.colors.ListedColormap` name
(`'Set2'`, `'tab20'`, …) or a :class:`~cycler.Cycler` object.
It is possible to specify a list of the same size as `color` to choose
a different color map for each panel.
legend_loc
Location of legend, either `'on data'`, `'right margin'` or a valid keyword
for the `loc` parameter of :class:`~matplotlib.legend.Legend`.
ax
A matplotlib axes object or a list with the same length as `color` thereof.
ncols
Number of columns for multi-panel plots
show
If True, show the firgure. If false, return a list of Axes objects
wspace
Adjust the width of the space between multiple panels.
hspace
Adjust the height of the space between multiple panels.
**kwargs
Arguments to pass to :func:`scanpy.pl.embedding`.
Returns
-------
axes
A list of axes objects, containing one
element for each `color`, or None if `show == True`.
See also
--------
:func:`scanpy.pl.embedding`
"""
adata._sanitize()
def _make_iterable(var, singleton_types=(str,)):
return (
itertools.repeat(var)
if isinstance(var, singleton_types) or var is None
else list(var)
)
color = [color] if isinstance(color, str) or color is None else list(color)
basis = _make_iterable(basis)
legend_loc = _make_iterable(legend_loc)
palette = _make_iterable(palette, (str, Cycler))
# set-up grid, if no axes are provided
if ax is None:
n_panels = len(color)
nrows = int(np.ceil(float(n_panels) / ncols))
ncols = np.min((n_panels, ncols))
hspace = (
rcParams.get("figure.subplot.hspace", 0.0) if hspace is None else hspace
)
wspace = (
rcParams.get("figure.subplot.wspace", 0.0) if wspace is None else wspace
)
# Don't ask about +/- 1 but appears to be most faithful to the panel size
fig_width = panel_size[0] * ncols + hspace * (ncols + 1)
fig_height = panel_size[1] * nrows + wspace * (nrows - 1)
fig, axs = plt.subplots(
nrows=nrows,
ncols=ncols,
figsize=(fig_width, fig_height),
gridspec_kw={"wspace": wspace, "hspace": hspace},
squeeze=False,
)
axs = axs.flatten()
else:
axs = [ax] if not isinstance(ax, Sequence) else list(ax)
fig = axs[0].get_figure()
# use the scanpy plotting api to fill individual components
for ax, tmp_color, tmp_basis, tmp_legend_loc, tmp_palette in zip(
axs, color, basis, legend_loc, palette
):
# cycle colors for categories with many values instead of
# coloring them in grey
if tmp_palette is None and tmp_color is not None:
if str(adata.obs[tmp_color].dtype) == "category":
if adata.obs[tmp_color].unique().size > len(sc.pl.palettes.default_102):
tmp_palette = cycler(color=sc.pl.palettes.default_102)
add_labels = tmp_legend_loc == "on data"
tmp_legend_loc = None if add_labels else tmp_legend_loc
sc.pl.embedding(
adata,
tmp_basis,
ax=ax,
show=False,
color=tmp_color,
legend_loc=tmp_legend_loc,
palette=tmp_palette,
**kwargs,
)
# manually add labels for "on data", as missing entries in `obsm` will cause
# a flood of matplotlib warnings.
# TODO: this could eventually be fixed upstream in scanpy
if add_labels:
_add_labels(
ax,
adata.obsm["X_" + tmp_basis],
adata.obs[tmp_color].values,
legend_fontweight=kwargs.get("legend_fontweight", "bold"),
legend_fontsize=kwargs.get("legend_fontsize", None),
legend_fontoutline=kwargs.get("legend_fontoutline", None),
),
# hide unused panels in grid
for ax in axs[len(color) :]:
ax.axis("off")
if show:
fig.show()
else:
# only return axes that actually contain a plot.
return axs[: len(color)]
def test_slicing_remove_unused_categories():
adata = AnnData(
np.array([[1, 2], [3, 4], [5, 6], [7, 8]]),
dict(k=['a', 'a', 'b', 'b']))
adata._sanitize()
assert adata[3:5].obs['k'].cat.categories.tolist() == ['b']
def _indexed_expression_df(
adata: AnnData,
var_names: Optional[Union[_VarNames, Mapping[str, _VarNames]]] = None,
groupby: Optional[Union[str, Sequence[str]]] = None,
use_raw: Optional[bool] = None,
log: bool = False,
num_categories: int = 7,
layer: Optional[str] = None,
gene_symbols: Optional[str] = None,
concat_indices: bool = True,
):
"""
Given the anndata object, prepares a data frame in which the row index are the categories
defined by group by and the columns correspond to var_names.
Parameters
----------
adata
Annotated data matrix.
var_names
`var_names` should be a valid subset of `adata.var_names`. All genes are used if no
given.
groupby
The key of the observation grouping to consider. It is expected that
groupby is a categorical. If groupby is not a categorical observation,
it would be subdivided into `num_categories`.
use_raw
Use `raw` attribute of `adata` if present.
log
Use the log of the values
num_categories
Only used if groupby observation is not categorical. This value
determines the number of groups into which the groupby observation
should be subdivided.
gene_symbols
Key for field in .var that stores gene symbols.
concat_indices
Concatenates categorical indices into a single categorical index, if
groupby is a sequence. True by default.
Returns
-------
Tuple of `pandas.DataFrame` and list of categories.
"""
from scipy.sparse import issparse
adata._sanitize()
if use_raw is None and adata.raw is not None:
use_raw = True
if isinstance(var_names, str):
var_names = [var_names]
if var_names is None:
if use_raw:
var_names = adata.raw.var_names.values
else:
var_names = adata.var_names.values
if groupby is not None:
if isinstance(groupby, str):
# if not a list, turn into a list
groupby = [groupby]
for group in groupby:
if group not in adata.obs_keys():
raise ValueError(
'groupby has to be a valid observation. '
f'Given {group}, is not in observations: {adata.obs_keys()}'
)
if gene_symbols is not None and gene_symbols in adata.var.columns:
# translate gene_symbols to var_names
# slow method but gives a meaningful error if no gene symbol is found:
translated_var_names = []
# if we're using raw to plot, we should also do gene symbol translations
# using raw
if use_raw:
adata_or_raw = adata.raw
else:
adata_or_raw = adata
for symbol in var_names:
if symbol not in adata_or_raw.var[gene_symbols].values:
logg.error(f"Gene symbol {symbol!r} not found in given "
f"gene_symbols column: {gene_symbols!r}")
return
translated_var_names.append(adata_or_raw.var[
adata_or_raw.var[gene_symbols] == symbol].index[0])
symbols = var_names
var_names = translated_var_names
if layer is not None:
if layer not in adata.layers.keys():
raise KeyError(
f'Selected layer: {layer} is not in the layers list. '
f'The list of valid layers is: {adata.layers.keys()}')
matrix = adata[:, var_names].layers[layer]
elif use_raw:
matrix = adata.raw[:, var_names].X
else:
matrix = adata[:, var_names].X
if issparse(matrix):
matrix = matrix.toarray()
if log:
matrix = np.log1p(matrix)
obs_tidy = pd.DataFrame(matrix, columns=var_names)
if groupby is None:
groupby = ''
obs_tidy_idx = pd.Series(np.repeat('',
len(obs_tidy))).astype('category')
idx_categories = obs_tidy_idx.cat.categories
else:
if len(groupby) == 1 and not is_categorical_dtype(
adata.obs[groupby[0]]):
# if the groupby column is not categorical, turn it into one
# by subdividing into `num_categories` categories
obs_tidy_idx = pd.cut(adata.obs[groupby[0]], num_categories)
idx_categories = obs_tidy_idx.cat.categories
else:
assert all(
is_categorical_dtype(adata.obs[group]) for group in groupby)
if concat_indices:
obs_tidy_idx = adata.obs[groupby[0]]
if len(groupby) > 1:
for group in groupby[1:]:
# create new category by merging the given groupby categories
obs_tidy_idx = (
obs_tidy_idx.astype(str) + "_" +
adata.obs[group].astype(str)).astype('category')
obs_tidy_idx.name = "_".join(groupby)
idx_categories = obs_tidy_idx.cat.categories
else:
obs_tidy_idx = [adata.obs[group]
for group in groupby] # keep as multiindex
idx_categories = [x.cat.categories for x in obs_tidy_idx]
obs_tidy.set_index(obs_tidy_idx, inplace=True)
if gene_symbols is not None:
# translate the column names to the symbol names
obs_tidy.rename(
columns={var_names[x]: symbols[x]
for x in range(len(var_names))},
inplace=True,
)
return idx_categories, obs_tidy
def clonotype_network(
adata: AnnData,
*,
color: Union[str, Sequence[str], None] = None,
basis: str = "clonotype_network",
panel_size: Tuple[float, float] = (10, 10),
color_by_n_cells: bool = False,
scale_by_n_cells: bool = True,
base_size: Optional[float] = None,
size_power: Optional[float] = None,
use_raw: Optional[bool] = None,
show_labels: bool = True,
label_fontsize: Optional[int] = None,
label_fontweight: str = "bold",
label_fontoutline: int = 3,
label_alpha: float = 0.6,
label_y_offset: float = 2,
legend_fontsize=None,
legend_width=2,
show_legend: Optional[bool] = None,
show_size_legend: bool = True,
palette: Union[str, Sequence[str], Cycler, None] = None,
cmap: Union[str, Colormap] = None,
edges_color: Union[str, None] = None,
edges_cmap: Union[Colormap, str] = COLORMAP_EDGES,
edges: bool = True,
edges_width: float = 0.4,
frameon: Optional[bool] = None,
title: Optional[str] = None,
ax: Optional[Axes] = None,
fig_kws: Optional[dict] = None,
) -> plt.Axes:
"""\
Plot the :term:`Clonotype` network.
Requires running :func:`scirpy.tl.clonotype_network` first, to
compute the layout.
{clonotype_network}
When the network is colored by continuous variables (genes, or numeric columns
from `obs`), the average of the cells in each dot is computed. When the network
is colored by categorical variables (categorical columns from `obs`), different
categories per dot are visualized as pie chart.
The layouting algorithm of :func:`scirpy.tl.clonotype_network` takes point sizes
into account. For this reason, we recommend providing `base_size` and `size_power`
already to the tool function.
Parameters
----------
adata
Annotated data matrix.
color
Keys for annotations of observations/cells or variables/genes,
e.g. `patient` or `CD8A`.
basis
Key under which the graph layout coordinates are stored in `adata.obsm`.
panel_size
Size of the main figure panel in inches.
color_by_n_cells
Color the nodes by the number of cells they represent. This overrides
the `color` option.
scale_by_n_cells
Scale the nodes by the number of cells they represent. If this is
set to `True`, we recommend using a "size-aware" layout in
:func:`scirpy.tl.clonotype_network` to avoid overlapping nodes (default).
base_size
Size of a point representing 1 cell. Per default, the value provided
to :func:`scirpy.tl.clonotype_network` is used. This option allows to
override this value without recomputing the layout.
size_power
Point sizes are raised to the power of this value. Per default, the
value provided to :func:`scirpy.tl.clonotype_network` is used. This option
allows to override this value without recomputing the layout.
use_raw
Use `adata.raw` for plotting gene expression values. Default: Use `adata.raw`
if it exists, and `adata` otherwise.
show_labels
If `True` plot clonotype ids on top of the subnetworks.
label_fontsize
Fontsize for the clonotype labels
label_fontweight
Fontweight for the clonotype labels
label_fontoutline
Size of the fontoutline added to the clonotype labels. Set to `None` to disable.
label_alpha
Transparency of the clonotype labels
label_y_offset
Offset the clonotype label on the y axis for better visibility of the
subnetworks.
legend_fontsize
Font-size for the legend.
show_legend
Whether to show a legend (when plotting categorical variables)
or a colorbar (when plotting continuous variables) on the right margin.
Per default, a legend is shown if the number of categories is smaller than
50, other wise no legend is shown.
show_legend_size
Whether to show a legend for dot sizes on the right margin.
This option is only applicable if `scale_by_n_cells` is `True`.
palette
Colors to use for plotting categorical annotation groups.
The palette can be a valid :class:`~matplotlib.colors.ListedColormap` name
(`'Set2'`, `'tab20'`, …) or a :class:`~cycler.Cycler` object.
a different color map for each panel.
cmap
Colormap to use for plotting continuous variables.
edges_color
Color of the edges. Set to `None` to color by connectivity and use the
color map provided by `edges_cmap`.
edges_cmap
Colormap to use for coloring edges by connectivity.
edges
Whether to show the edges or not.
edges_width
width of the edges
frameon
Whether to show a frame around the plot
title
The main plot title
ax
Add the plot to a predefined Axes object.
cax
Add the colorbar (if any) to this predefined Axes object.
fig_kws
Parameters passed to the :func:`matplotlib.pyplot.figure` call
if no `ax` is specified.
Returns
-------
A list of axes objects, containing one
element for each `color`, or None if `show == True`.
"""
# The plotting code borrows a lot from scanpy.plotting._tools.paga._paga_graph.
adata._sanitize()
try:
clonotype_key = adata.uns[basis]["clonotype_key"]
base_size = adata.uns[basis][
"base_size"] if base_size is None else base_size
size_power = (adata.uns[basis]["size_power"]
if size_power is None else size_power)
except KeyError:
raise KeyError(
f"{basis} not found in `adata.uns`. Did you run `tl.clonotype_network`?"
)
if f"X_{basis}" not in adata.obsm_keys():
raise KeyError(
f"X_{basis} not found in `adata.obsm`. Did you run `tl.clonotype_network`?"
)
if clonotype_key not in adata.obs.columns:
raise KeyError(f"{clonotype_key} not found in adata.obs.")
if clonotype_key not in adata.uns:
raise KeyError(f"{clonotype_key} not found in adata.uns.")
if use_raw is None:
use_raw = adata.raw is not None
if frameon is None:
frameon = settings._frameon
if show_legend is None:
if color in adata.obs.columns and is_categorical_dtype(
adata.obs[color]):
show_legend = adata.obs[color].nunique() < 50
else:
show_legend = True
clonotype_res = adata.uns[clonotype_key]
coords, adj_mat = _graph_from_coordinates(adata, clonotype_key)
nx_graph = nx.Graph(_distance_to_connectivity(adj_mat))
# Prepare figure
if ax is None:
fig_kws = dict() if fig_kws is None else fig_kws
fig_width = (panel_size[0] if not (show_legend or show_size_legend)
else panel_size[0] + legend_width + 0.5)
fig_kws.update({"figsize": (fig_width, panel_size[1])})
ax = _init_ax(fig_kws)
if title is None and color is not None:
title = color
ax.set_frame_on(frameon)
ax.set_xticks([])
ax.set_yticks([])
_plot_clonotype_network_panel(
adata,
ax,
legend_width=legend_width,
color=color,
coords=coords,
use_raw=use_raw,
cell_indices=clonotype_res["cell_indices"],
nx_graph=nx_graph,
show_legend=show_legend,
show_size_legend=show_size_legend,
show_labels=show_labels,
label_fontsize=label_fontsize,
label_fontoutline=label_fontoutline,
label_fontweight=label_fontweight,
legend_fontsize=legend_fontsize,
base_size=base_size,
size_power=size_power,
cmap=cmap,
edges=edges,
edges_width=edges_width,
edges_color=edges_color,
edges_cmap=edges_cmap,
title=title,
palette=palette,
label_alpha=label_alpha,
label_y_offset=label_y_offset,
scale_by_n_cells=scale_by_n_cells,
color_by_n_cells=color_by_n_cells,
)
return ax