fix new counts

app.py

@@ -173,7 +173,7 @@ def perturb(gene, locus1, locus2):
     # get integer index of gene
     gene_idx = gene_idx_map[gene]
     rna.obs['log2FC'] = ism[:, gene_idx]
-    rna.layers['new_counts'] = perterbed_rna_recon
+    rna.obs['new_counts'] = perterbed_rna_recon[:, gene_idx]
     
     fig = sc.pl.umap(rna, 
                      color=['celltype', 'log2FC'], 
@@ -203,7 +203,7 @@ def perturb(gene, locus1, locus2):
     violin_img = violin_img[:, :, [1, 2, 3, 0]]
 
     fig, ax = plt.subplots(figsize=(6, 3))
-    sc.pl.violin(rna, gene, groupby='celltype', layer='new_counts', show=False, ax=ax)
+    sc.pl.violin(rna, 'new_counts', groupby='celltype', show=False, ax=ax)
     ax.set_title(f'{gene} expression after perturbation')
     fig.canvas.draw()
     violin_img_new = np.frombuffer(fig.canvas.tostring_argb(), dtype=np.uint8)