scanpy spot_size参数

example1

from anndata import AnnData
import scanpy as sc
import squidpy as sq
import numpy as np
from numpy.random import default_rng

import matplotlib.pyplot as plt

sc.logging.print_header()
print(f"squidpy=={sq.__version__}")

rng = default_rng(42)
counts = rng.integers(0, 15, size=(10, 100))  # feature matrix
coordinates = rng.uniform(0, 10, size=(10, 2))  # spatial coordinates
image = rng.uniform(0, 1, size=(10, 10, 3))  # image

spot_size=1

adata = AnnData(counts, obsm={"spatial": coordinates}, dtype=np.int64)
sc.pp.normalize_total(adata)
sc.pp.log1p(adata)
sc.pp.pca(adata)
sc.pp.neighbors(adata)
sc.tl.umap(adata)
sc.tl.leiden(adata)
adata

fig, axs = plt.subplots(1, 1)
sc.pl.spatial(adata, color="leiden",spot_size=1,ax = axs, show=False)
axs.set_xscale('linear')#x轴设置刻度
axs.set_yscale('linear')#y轴设置刻度
plt.show()

spot_size=2

adata = AnnData(counts, obsm={"spatial": coordinates}, dtype=np.int64)
sc.pp.normalize_total(adata)
sc.pp.log1p(adata)
sc.pp.pca(adata)
sc.pp.neighbors(adata)
sc.tl.umap(adata)
sc.tl.leiden(adata)
adata

fig, axs = plt.subplots(1, 1)
sc.pl.spatial(adata, color="leiden",spot_size=2,ax = axs, show=False)
axs.set_xscale('linear')#x轴设置刻度
axs.set_yscale('linear')#y轴设置刻度
plt.show()