Ken Furudate

import scanpy as sc
import anndata as ad
import squidpy as sq

import numpy as np
import pandas as pd

import matplotlib as mpl
from matplotlib import pyplot as plt
%matplotlib inline
import matplotlib.font_manager
plt.rcParams['font.sans-serif'] = ['Arial'] + plt.rcParams['font.sans-serif']
plt.rcParams["font.size"] = 20

import os
import seaborn as sns
from pathlib import Path

from IPython.core.display import display, HTML
display(HTML("<style>.container { width:80% !important; }</style>"))

import warnings
warnings.filterwarnings('ignore')

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

import skimage

/usr/local/lib/python3.7/dist-packages/distributed/config.py:20: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  defaults = yaml.load(f)

scanpy==1.9.1 anndata==0.8.0 umap==0.5.3 numpy==1.21.6 scipy==1.4.1 pandas==1.3.5 scikit-learn==1.0.2 statsmodels==0.13.2 python-igraph==0.9.11 pynndescent==0.5.7
squidpy==1.2.2

datadir="/data/spatial/"
in_f = "integrated_data.h5ad"

data = sc.read_h5ad(datadir + in_f)

set(data.obs['sample'])

{'A', 'B', 'C', 'D'}

adata = data[data.obs['sample']=="A"]
bdata = data[data.obs['sample']=="B"]
cdata = data[data.obs['sample']=="C"]
ddata = data[data.obs['sample']=="D"]

data_lst = (adata, bdata, cdata, ddata)

interested_genes = [
 # Exhausted T cell marker
 "NR4A2", "TOX", "BACH2",
 
 # Cytotoxic T cell marker                    
 "CD8A", "CD28"
]

vmax_ = [1.6, 0.8, 0.1, 0.4, 0.1]

idx = 1
sc.pl.spatial(adata=data_lst[idx], 
              color=interested_genes,
              color_map="viridis",
              vmax=vmax_,
              ncols=3,
              na_in_legend=False,
              )

interested_genes = [
  # Regulatory T cell marker
  "CD4", "FOXP3", "IL2RA",
  
  # M2 like TAM markers 
  "CD163", "MSR1",  "MRC1"
]

vmax_ = [0.7, 0.1, 0.2, 0.7, 0.2, 0.2]

idx = 1
sc.pl.spatial(adata=data_lst[idx], 
              color=interested_genes,
              color_map="viridis",
              vmax=vmax_,
              ncols=3,
              na_in_legend=False,
              )