from matplotlib import pyplot as plt
from PIL import Image
import pandas as pd
import matplotlib
import numpy as np
from stlearn._compat import Literal
from typing import Optional, Union
from anndata import AnnData
import warnings
# from .utils import get_img_from_fig, checkType
import scanpy
[docs]def non_spatial_plot(
adata: AnnData,
use_label: str = "louvain",
) -> Optional[AnnData]:
"""\
A wrap function to plot all the non-spatial plot from scanpy.
This function will produce 3 plots: PAGA graph, cluster plot in PAGA space and
DPT in PAGA space.
Parameters
----------
adata
Annotated data matrix.
use_label
Use label result of cluster method.
dpi
Set dpi as the resolution for the plot.
Returns
-------
Nothing
"""
# plt.rcParams['figure.dpi'] = dpi
if "paga" in adata.uns.keys():
# adata.uns[use_label+"_colors"] = adata.uns["tmp_color"]
print("PAGA plot:")
scanpy.pl.paga(adata, color=use_label)
scanpy.tl.draw_graph(adata, init_pos="paga")
# adata.uns[use_label+"_colors"] = adata.uns["tmp_color"]
print("Gene expression (reduced dimension) plot:")
scanpy.pl.draw_graph(adata, color=use_label, legend_loc="on data")
print("Diffusion pseudotime plot:")
scanpy.pl.draw_graph(adata, color="dpt_pseudotime")
else:
scanpy.pl.draw_graph(adata)
# adata.uns[use_label+"_colors"] = adata.uns["tmp_color"]
scanpy.pl.draw_graph(adata, color=use_label, legend_loc="on data")