scanpy sc.pl.scatter学习

# !mkdir data
# !wget http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz -O data/pbmc3k_filtered_gene_bc_matrices.tar.gz
# !cd data; tar -xzf pbmc3k_filtered_gene_bc_matrices.tar.gz
# !mkdir write

import numpy as np
import pandas as pd
import scanpy as sc

sc.settings.verbosity = 3             # verbosity: errors (0), warnings (1), info (2), hints (3)
sc.logging.print_header()
sc.settings.set_figure_params(dpi=80, facecolor='white')

results_file = 'write/pbmc3k.h5ad'  # the file that will store the analysis results

adata = sc.read_10x_mtx(
    'data/filtered_gene_bc_matrices/hg19/',  # the directory with the `.mtx` file
    var_names='gene_symbols',                # use gene symbols for the variable names (variables-axis index)
    cache=True)                              # write a cache file for faster subsequent reading

adata.var_names_make_unique()  # this is unnecessary if using `var_names='gene_ids'` in `sc.read_10x_mtx

adata

# preprocessing

sc.pl.highest_expr_genes(adata, n_top=20, )

sc.pp.filter_cells(adata, min_genes=200)
sc.pp.filter_genes(adata, min_cells=3)

adata.var['mt'] = adata.var_names.str.startswith('MT-')  # annotate the group of mitochondrial genes as 'mt'
sc.pp.calculate_qc_metrics(adata, qc_vars=['mt'], percent_top=None, log1p=False, inplace=True)

sc.pl.violin(adata, ['n_genes_by_counts', 'total_counts', 'pct_counts_mt'],
             jitter=0.4, multi_panel=True)

sc.pl.scatter(adata, x='total_counts', y='pct_counts_mt')
sc.pl.scatter(adata, x='total_counts', y='n_genes_by_counts')



# tips = sns.load_dataset('tips')

# sns.scatterplot(x='total_bill', y='tip',data=tips)

# tips

而自己用seaborn实现

df1=adata.obs[["total_counts",'pct_counts_mt']]
import seaborn as sns
sns.scatterplot(data=df1,x="total_counts",y="pct_counts_mt")# 必须需要加入data=df1,不能直接传入df1 
## 这个scatter是一样的

其实sc.pl.scatter和sns.scatterplot()是一样的，并没有设么区别