<jupyter_start><jupyter_text>IL_genes = list(adata.var.index[adata.var.index.str.contains("IL")])sc.pl.umap(adata, color = IL_genes)  Analysis<jupyter_code>filename = 'Current.h5ad'
adata = sc.read_h5ad(filename)
fig, ax = plt.subplots(1,1)
plt.hist(adata.obs.n_counts, histtype='step', color = 'k')
plt.hist(adata.obs.n_counts, histtype='stepfilled', color = 'k', alpha = 0.2)
plt.title('Uniquely Mapped Reads')
adata.obs
g = sns.violinplot(data = adata.obs, x ='n_counts', y = 'Treatment', hue = 'Experimental_Label')
g.figure.savefig('figures/N_counts', transparent=True)
g = sns.violinplot(data = adata.obs, x ='n_genes', y = 'Treatment', hue = 'Experimental_Label')
adata.obs.columns
g.figure.savefig('figures/N_genes', transparent=True)
variable = 'phase'
sc.pl.umap(adata, color = variable, title = 'Cell Cycle Phase', frameon = False, size = 200, alpha=0.6, save = variable)<jupyter_output>WARNING: saving figure to file figures/umapphase.pdf
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