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Make scplot compatible with pegasusio #6

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Make scplot compatible with pegasusio #6

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54 changes: 40 additions & 14 deletions scplot/plot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import pandas as pd
import scipy.sparse
from anndata import AnnData
from pegasusio import MultimodalData
from holoviews import dim
from holoviews.plotting.bokeh.callbacks import LinkCallback
from holoviews.plotting.links import Link
Expand All @@ -33,7 +34,7 @@ class __BrushLinkCallbackRange(LinkCallback):
target_handles = ['cds', 'glyph']

source_code = """

target_selected.indices = source_selected.indices;
"""

Expand Down Expand Up @@ -305,7 +306,7 @@ def __bin(df, nbins, coordinate_columns, reduce_function, coordinate_column_to_r
return df.groupby(coordinate_columns, as_index=False).agg(agg_func), df[coordinate_columns]


def violin(adata: AnnData, keys: Union[str, List[str], Tuple[str]], by: str = None,
def violin(adata: Union[AnnData, MultimodalData], keys: Union[str, List[str], Tuple[str]], by: str = None,
width: int = 300, cmap: Union[str, List[str], Tuple[str]] = None, cols: int = None,
use_raw: bool = None, **kwds) -> hv.core.element.Element:
"""
Expand All @@ -322,6 +323,8 @@ def violin(adata: AnnData, keys: Union[str, List[str], Tuple[str]], by: str = No
"""
if cols is None:
cols = 3
if not isinstance(adata, AnnData):
adata = adata.to_anndata()
adata_raw = __get_raw(adata, use_raw)
keys = __to_list(keys)
df = __get_df(adata, adata_raw, keys + ([] if by is None else [by]))
Expand All @@ -342,7 +345,7 @@ def violin(adata: AnnData, keys: Union[str, List[str], Tuple[str]], by: str = No
return layout


def heatmap(adata: AnnData, keys: Union[str, List[str], Tuple[str]], by: str,
def heatmap(adata: Union[AnnData, MultimodalData], keys: Union[str, List[str], Tuple[str]], by: str,
reduce_function: Callable[[np.ndarray], float] = np.mean,
use_raw: bool = None, cmap: Union[str, List[str], Tuple[str]] = 'Reds', **kwds) -> hv.core.element.Element:
"""
Expand All @@ -357,6 +360,8 @@ def heatmap(adata: AnnData, keys: Union[str, List[str], Tuple[str]], by: str,
use_raw: Use `raw` attribute of `adata` if present.
"""

if not isinstance(adata, AnnData):
adata = adata.to_anndata()
adata_raw = __get_raw(adata, use_raw)
keys = __to_list(keys)
df = None
Expand All @@ -378,7 +383,7 @@ def heatmap(adata: AnnData, keys: Union[str, List[str], Tuple[str]], by: str,
return df.hvplot.heatmap(x='feature', y=by, C='value', reduce_function=reduce_function, **keywords)


def scatter(adata: AnnData, x: str, y: str, color: str = None, size: Union[int, str] = None,
def scatter(adata: Union[AnnData, MultimodalData], x: str, y: str, color: str = None, size: Union[int, str] = None,
dot_min=2, dot_max=14, use_raw: bool = None, sort: bool = True, width: int = 400, height: int = 400,
nbins: int = -1, reduce_function: Callable[[np.array], float] = np.max,
cmap: Union[str, List[str], Tuple[str]] = None, palette: Union[str, List[str], Tuple[str]] = None,
Expand All @@ -403,6 +408,8 @@ def scatter(adata: AnnData, x: str, y: str, color: str = None, size: Union[int,
nbins: Number of bins used to summarize plot on a grid. Useful for large datasets. Negative one means automatically bin the plot.
reduce_function: Function used to summarize overlapping cells if nbins is specified
"""
if not isinstance(adata, AnnData):
adata = adata.to_anndata()
return __scatter(adata=adata, x=x, y=y, color=color, size=size, dot_min=dot_min, dot_max=dot_max, use_raw=use_raw,
sort=sort, width=width, height=height, nbins=nbins, reduce_function=reduce_function, cmap=cmap, palette=palette,
is_scatter=True, **kwds)
Expand Down Expand Up @@ -527,7 +534,7 @@ def __scatter(adata: AnnData, x: str, y: str, color=None, size: Union[int, str]
return return_value


def dotplot(adata: AnnData, keys: Union[str, List[str], Tuple[str]], by: str,
def dotplot(adata: Union[AnnData, MultimodalData], keys: Union[str, List[str], Tuple[str]], by: str,
reduce_function: Callable[[np.ndarray], float] = np.mean,
fraction_min: float = 0, fraction_max: float = None, dot_min: int = 1, dot_max: int = 26,
use_raw: bool = None, cmap: Union[str, List[str], Tuple[str]] = 'Reds',
Expand All @@ -549,6 +556,8 @@ def dotplot(adata: AnnData, keys: Union[str, List[str], Tuple[str]], by: str,
sort_function: Optional function that accepts summarized data frame and returns a list of row indices in the order to render in the heatmap.
"""

if not isinstance(adata, AnnData):
adata = adata.to_anndata()
adata_raw = __get_raw(adata, use_raw)
keys = __to_list(keys)
keywords = dict(colorbar=True, ylabel=str(by), xlabel='', padding=0, rot=90, cmap=cmap)
Expand Down Expand Up @@ -634,7 +643,7 @@ def non_zero(g):
return result


def scatter_matrix(adata: AnnData, keys: Union[str, List[str], Tuple[str]], color=None, use_raw: bool = None,
def scatter_matrix(adata: Union[AnnData, MultimodalData], keys: Union[str, List[str], Tuple[str]], color=None, use_raw: bool = None,
**kwds) -> hv.core.element.Element:
"""
Generate a scatter plot matrix.
Expand All @@ -646,6 +655,8 @@ def scatter_matrix(adata: AnnData, keys: Union[str, List[str], Tuple[str]], colo
use_raw: Use `raw` attribute of `adata` if present.
"""

if not isinstance(adata, AnnData):
adata = adata.to_anndata()
adata_raw = __get_raw(adata, use_raw)
keys = __to_list(keys)
if color is not None:
Expand Down Expand Up @@ -680,7 +691,7 @@ def __fix_scatter_colors(adata, df_to_plot, key, is_color_by_numeric, cmap, pale
del keywords[color_keyword_delete]


def embedding(adata: AnnData, basis: Union[str, List[str], Tuple[str]],
def embedding(adata: Union[AnnData, MultimodalData], basis: Union[str, List[str], Tuple[str]],
keys: Union[None, str, List[str], Tuple[str]] = None,
cmap: Union[str, List[str], Tuple[str]] = None, palette: Union[str, List[str], Tuple[str]] = None,
alpha: float = 1, size: float = None, width: int = 400, height: int = 400, sort: bool = True,
Expand Down Expand Up @@ -719,6 +730,8 @@ def embedding(adata: AnnData, basis: Union[str, List[str], Tuple[str]],
if keys is None:
keys = []
basis = __to_list(basis)
if not isinstance(adata, AnnData):
adata = adata.to_anndata()
adata_raw = __get_raw(adata, use_raw)
keys = __to_list(keys)
if tooltips is None:
Expand Down Expand Up @@ -812,17 +825,24 @@ def embedding(adata: AnnData, basis: Union[str, List[str], Tuple[str]],
return layout


def variable_feature_plot(adata: AnnData, **kwds) -> hv.core.element.Element:
def variable_feature_plot(adata: Union[AnnData, MultimodalData], **kwds) -> hv.core.element.Element:
"""
Generate a variable feature plot.

Args:
adata: Annotated data matrix.
"""

if 'hvf_loess' in adata.var:
keywords = dict(x='mean', y='var', y_fit='hvf_loess', color='highly_variable_features',
xlabel='Mean log expression', ylabel='Variance of log expression')
if not isinstance(adata, AnnData):
adata = adata.to_anndata()

if 'hvf_flavor' in adata.uns.keys():
if adata.uns['hvf_flavor'] == 'pegasus':
keywords = dict(x='mean', y='var', y_fit='hvf_loess', color='highly_variable_features',
xlabel='Mean log expression', ylabel='Variance of log expression')
else:
keywords = dict(x='mean', y='dispersion_norm', y_fit=None, color='highly_variable_features',
xlabel='Mean log expression', ylabel='Normalized dispersion')
else:
keywords = dict(x='means', y='dispersions_norm', y_fit=None, color='highly_variable',
xlabel='Mean log expression', ylabel='Normalized dispersion')
Expand All @@ -842,10 +862,14 @@ def variable_feature_plot(adata: AnnData, **kwds) -> hv.core.element.Element:
return scatter(adata, x=x, y=y, xlabel=xlabel, color=color,
ylabel=ylabel, **keywords) * line(adata, x=x, y=y_fit, line_color=line_color)
else:
return scatter(adata, x=x, y=y, color=color, xlabel=xlabel, ylabel=ylabel)
if 'robust' in adata.var:
return scatter(adata[:, adata.var['robust']], x=x, y=y, color=color,
xlabel=xlabel, ylabel=ylabel)
else:
return scatter(adata, x=x, y=y, color=color, xlabel=xlabel, ylabel=ylabel)


def volcano(adata: AnnData, basis: str = 'de_res', x: str = 'log_fold_change', y: str = 't_qval',
def volcano(adata: Union[AnnData, MultimodalData], basis: str = 'de_res', x: str = 'log_fold_change', y: str = 't_qval',
x_cutoff: float = 1, y_cutoff: float = 0.05, cluster_ids: Union[List, Tuple, Set] = None,
**kwds) -> hv.core.element.Element:
"""
Expand Down Expand Up @@ -921,7 +945,7 @@ def volcano(adata: AnnData, basis: str = 'de_res', x: str = 'log_fold_change', y
return result


def composition_plot(adata: AnnData, by: str, condition: str, stacked: bool = True, normalize: bool = True,
def composition_plot(adata: Union[AnnData, MultimodalData], by: str, condition: str, stacked: bool = True, normalize: bool = True,
condition_sort_by: str = None, cmap: Union[str, List[str], Tuple[str]] = None,
**kwds) -> hv.core.element.Element:
"""
Expand All @@ -937,6 +961,8 @@ def composition_plot(adata: AnnData, by: str, condition: str, stacked: bool = Tr
cmap: Color map name (hv.plotting.list_cmaps()) or a list of hex colors. See http://holoviews.org/user_guide/Styling_Plots.html for more information.
"""

if not isinstance(adata, AnnData):
adata = adata.to_anndata()
adata_raw = __get_raw(adata, False)
keys = [by, condition]
adata_df = __get_df(adata, adata_raw, keys)
Expand Down
1 change: 1 addition & 0 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@

requirements = [
'anndata',
'pegasusio',
'colorcet',
'holoviews',
'hvplot',
Expand Down