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Runtime error
Runtime error
Commit ·
d1a5128
1
Parent(s): 32e7db6
test recon mean as original violin
Browse files
app.py
CHANGED
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@@ -356,6 +356,7 @@ def perturb(gene, locus1, locus2, use_max_gene):
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else:
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gene_idx = gene_idx_map[gene]
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rna.obs['log2FC'] = ism[:, gene_idx]
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rna.obs['new_mean'] = perterbed_rna_recon[:, gene_idx]
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fig = sc.pl.umap(rna,
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@@ -378,7 +379,8 @@ def perturb(gene, locus1, locus2, use_max_gene):
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image_from_plot = image_from_plot[:, :, [1, 2, 3, 0]]
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fig, ax = plt.subplots(figsize=(6, 4))
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sc.pl.violin(rna, max_gene if use_max_gene else gene, groupby='celltype', layer='counts', show=False, ax=ax, rotation=90)
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ax.set_title(f'Normal {max_gene if use_max_gene else gene} expression')
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fig.tight_layout()
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fig.canvas.draw()
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@@ -438,7 +440,8 @@ with gr.Blocks(theme='WeixuanYuan/Soft_dark') as demo:
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outputs = [out_img, out_violin, out_violin_new, out_violin_fc]
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gr.Examples(examples=[['INS', 'chr11:2,289,895', 'chr11:2,298,840', False],
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['
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['TSPAN1', 'TSPAN1', 'PIK3R3', False],
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['GCG', 'GCG', 'FAP', False],
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['KRT19', 'chr17:22,220,637', 'chr17:39,591,813', False],
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else:
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gene_idx = gene_idx_map[gene]
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rna.obs['log2FC'] = ism[:, gene_idx]
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rna.obs['old_mean'] = rna_recon[:, gene_idx]
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rna.obs['new_mean'] = perterbed_rna_recon[:, gene_idx]
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fig = sc.pl.umap(rna,
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image_from_plot = image_from_plot[:, :, [1, 2, 3, 0]]
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fig, ax = plt.subplots(figsize=(6, 4))
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#sc.pl.violin(rna, max_gene if use_max_gene else gene, groupby='celltype', layer='counts', show=False, ax=ax, rotation=90)
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sc.pl.violin(rna, 'old_mean', groupby='celltype', show=False, ax=ax, rotation=90)
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ax.set_title(f'Normal {max_gene if use_max_gene else gene} expression')
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fig.tight_layout()
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fig.canvas.draw()
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outputs = [out_img, out_violin, out_violin_new, out_violin_fc]
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gr.Examples(examples=[['INS', 'chr11:2,289,895', 'chr11:2,298,840', False],
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['OTUD3', 'chr1:20457786', 'chr1:20230413', False],
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['IRX2', 'chr5:2704405', 'chr5:2164879', False],
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['TSPAN1', 'TSPAN1', 'PIK3R3', False],
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['GCG', 'GCG', 'FAP', False],
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['KRT19', 'chr17:22,220,637', 'chr17:39,591,813', False],
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