from matplotlib import pyplot as plt
from PIL import Image
import pandas as pd
import matplotlib
import numpy as np
from typing import Optional, Union, Mapping # Special
from typing import Sequence, Iterable # ABCs
from typing import Tuple # Classes
from anndata import AnnData
import warnings
from .classes import GenePlot
from .classes_bokeh import BokehGenePlot
from ..utils import Empty, _empty, _AxesSubplot
from bokeh.io import push_notebook, output_notebook
from bokeh.plotting import show
[docs]def gene_plot(
adata: AnnData,
gene_symbols: Union[str, list] = None,
threshold: Optional[float] = None,
method: str = "CumSum",
contour: bool = False,
step_size: Optional[int] = None,
title: Optional["str"] = None,
figsize: Optional[Tuple[float, float]] = None,
cmap: Optional[str] = "Spectral_r",
use_label: Optional[str] = None,
list_clusters: Optional[list] = None,
ax: Optional[_AxesSubplot] = None,
show_plot: Optional[bool] = True,
show_axis: Optional[bool] = False,
show_image: Optional[bool] = True,
show_color_bar: Optional[bool] = True,
crop: Optional[bool] = True,
margin: Optional[bool] = 100,
size: Optional[float] = 7,
image_alpha: Optional[float] = 1.0,
cell_alpha: Optional[float] = 0.7,
use_raw: Optional[bool] = False,
fname: Optional[str] = None,
dpi: Optional[int] = 120,
) -> Optional[AnnData]:
GenePlot(
adata,
gene_symbols=gene_symbols,
threshold=threshold,
method=method,
contour=contour,
step_size=step_size,
title=title,
figsize=figsize,
cmap=cmap,
use_label=use_label,
list_clusters=list_clusters,
ax=ax,
show_plot=show_plot,
show_axis=show_axis,
show_image=show_image,
show_color_bar=show_color_bar,
crop=crop,
margin=margin,
size=size,
image_alpha=image_alpha,
cell_alpha=cell_alpha,
use_raw=use_raw,
fname=fname,
dpi=dpi,
)
[docs]def gene_plot_interactive(adata: AnnData):
bokeh_object = BokehGenePlot(adata)
output_notebook()
show(bokeh_object.app, notebook_handle=True)