CODEX

[1]:

import os
import pandas as pd
import numpy as np
import scanpy as sc
import anndata as ad

import matplotlib.pyplot as plt
import seaborn as sns

[2]:

import pysodb

[3]:

sc.set_figure_params(vector_friendly=False,format='pdf',transparent=True,dpi=50)
plt.rcParams["figure.figsize"] = (8, 8)

sns.set_style('white')

load a data using pysodb

[4]:

sodb = pysodb.SODB() # Initialization

/home/yzy/anaconda3/envs/SODB/lib/python3.9/site-packages/urllib3-1.26.12-py3.9.egg/urllib3/connectionpool.py:1045: InsecureRequestWarning: Unverified HTTPS request is being made to host 'gene.ai.tencent.com'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#ssl-warnings
  warnings.warn(

[ ]:

# this dataset is from publication "Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging"

[ ]:

# link in SODB: https://gene.ai.tencent.com/SpatialOmics/dataset?datasetID=59

[7]:

adata = sodb.load_experiment('Goltsev2028deep','MRL-5')
# the first parameter is the name of the dataset
# the second parameter is the name of one experiment in the dataset

download experiment[MRL-5] in dataset[Goltsev2028deep]

100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 69.6M/69.6M [00:07<00:00, 9.35MB/s]

load experiment[MRL-5] in dataset[Goltsev2028deep] from /home/yzy/anaconda3/envs/SODB/lib/python3.9/site-packages/pysodb-1.0.0-py3.9.egg/pysodb/cache/Goltsev2028deep/MRL-5.h5ad

identify clusters

[8]:

sc.pp.pca(adata)
sc.pp.neighbors(adata)
sc.tl.umap(adata)
sc.tl.leiden(adata, key_added="clusters")

/home/yzy/anaconda3/envs/SODB/lib/python3.9/site-packages/tqdm-4.64.1-py3.9.egg/tqdm/auto.py:22: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
  from .autonotebook import tqdm as notebook_tqdm

[9]:

sc.pl.umap(adata, color=[ "clusters"], wspace=0.4,
          add_outline=True,legend_fontsize=20, legend_fontoutline=2,
            legend_loc='on data',
            s=100
          )

../_images/scanpy_pysodb_scanpy_CODEX_11_0.png

[10]:

# plt.rcParams["figure.figsize"] = (8, 8)
sc.pl.embedding(adata, basis='spatial', color=['clusters'],show=False,size=10,add_outline=False)
plt.gca().set_aspect('equal', adjustable='box')

../_images/scanpy_pysodb_scanpy_CODEX_12_0.png

[12]:

# plt.rcParams["figure.figsize"] = (8, 8)
sc.pl.embedding(adata, basis='spatial', color=['ct'],show=False,size=10,add_outline=False)
plt.gca().set_aspect('equal', adjustable='box')

../_images/scanpy_pysodb_scanpy_CODEX_13_0.png

marker gene detection

[ ]:

sc.tl.rank_genes_groups(adata, "clusters", method="t-test")

[19]:

sc.pl.rank_genes_groups_tracksplot(adata, n_genes=3, groupby="clusters")

/home/yzy/anaconda3/envs/SODB/lib/python3.9/site-packages/scanpy-1.9.1-py3.9.egg/scanpy/plotting/_anndata.py:2414: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
  obs_tidy.index.value_counts(sort=False).iteritems()

../_images/scanpy_pysodb_scanpy_CODEX_16_1.png

[14]:

adata

[14]:

AnnData object with n_obs × n_vars = 73427 × 30
    obs: 'Imaging phenotype cluster ID', 'X.X', 'Y.Y', 'Z.Z', 'blank_Cy3_cyc15', 'blank_Cy5_cyc15', 'sample_Xtile_Ytile', 'niche cluster ID', 'Xtile', 'Ytile', 'sample', 'condition', 'ct', 'leiden', 'clusters'
    uns: 'leiden', 'leiden_colors', 'moranI', 'neighbors', 'pca', 'spatial_neighbors', 'umap', 'clusters_colors', 'ct_colors', 'rank_genes_groups', 'dendrogram_clusters'
    obsm: 'X_pca', 'X_umap', 'spatial', 'spatial_global'
    varm: 'PCs'
    obsp: 'connectivities', 'distances', 'spatial_connectivities', 'spatial_distances'

[15]:

marker_genes = adata.uns['rank_genes_groups']['names'][0]

[16]:

sc.pl.umap(adata, color=marker_genes, wspace=0.4,
          add_outline=True,legend_fontsize=10, legend_fontoutline=2,
            legend_loc='on data',
            s=80
          )

../_images/scanpy_pysodb_scanpy_CODEX_19_0.png

[17]:

# plt.rcParams["figure.figsize"] = (8, 8)
sc.pl.embedding(adata, basis='spatial', color=marker_genes,size=10,add_outline=True)

../_images/scanpy_pysodb_scanpy_CODEX_20_0.png