fix loo out of bounds from gene

app.py

@@ -103,7 +103,6 @@ def get_closest_peak_to_gene(gene_name, rna, peaks):
         return None
     chrom = loc["chrom"]
     chromStart = loc["chromStart"]
-    chromEnd = loc["chromEnd"]
     peaks['in_chr'] = peaks['chrom'] == chrom
     peaks['dist'] = peaks['chromStart'].apply(lambda s: abs(s - chromStart))
     peaks.loc[~peaks['in_chr'], 'dist'] = 1e9  # set distance to 1e9 if not in same chromosome
@@ -177,8 +176,6 @@ def get_heatmap_locus(gene, locus1, locus2, heatmap_range):
         print('Could not find loci', gene)
         return None
     chrom = loc["chrom"]
-    chromStart = loc["chromStart"]
-    chromEnd = loc["chromEnd"]
     if locus1.startswith('chr'):
         chrom = locus1.split(':')[0]
         pos1 = locus1.split(':')[1]
@@ -195,8 +192,8 @@ def get_heatmap_locus(gene, locus1, locus2, heatmap_range):
     a2_start = peaks.loc[a2, 'chromStart']
     interaction_dist = abs(a1_start - a2_start)
     chrom_size = beta_cooler.chromsizes[chrom]
-    locus_start = max(0, chromStart - interaction_dist - heatmap_range * 1000)
-    locus_end = min(chrom_size, chromEnd + interaction_dist + heatmap_range * 1000)
+    locus_start = max(0, a1_start - interaction_dist - heatmap_range * 1000)
+    locus_end = min(chrom_size, a2_start + interaction_dist + heatmap_range * 1000)
     heatmap_locus = f'{chrom}:{locus_start}-{locus_end}'
     heatmap_size = abs(locus_start - locus_end)
     res = '50kb'
@@ -382,7 +379,7 @@ def perturb(gene, locus1, locus2, use_max_gene):
 
     fig, ax = plt.subplots(figsize=(6, 4))
     sc.pl.violin(rna, gene, groupby='celltype', layer='counts', show=False, ax=ax, rotation=90)
-    ax.set_title(f'Normal {gene} expression')
+    ax.set_title(f'Normal {max_gene if use_max_gene else gene} expression')
     fig.tight_layout()
     fig.canvas.draw()
     violin_img = np.frombuffer(fig.canvas.tostring_argb(), dtype=np.uint8)
@@ -391,7 +388,7 @@ def perturb(gene, locus1, locus2, use_max_gene):
 
     fig, ax = plt.subplots(figsize=(6, 4))
     sc.pl.violin(rna, 'new_mean', groupby='celltype', show=False, ax=ax, rotation=90)
-    ax.set_title(f'{gene} expression after perturbation')
+    ax.set_title(f'{max_gene if use_max_gene else gene} expression after perturbation')
     fig.tight_layout()
     fig.canvas.draw()
     violin_img_new = np.frombuffer(fig.canvas.tostring_argb(), dtype=np.uint8)
@@ -400,7 +397,7 @@ def perturb(gene, locus1, locus2, use_max_gene):
 
     fig, ax = plt.subplots(figsize=(6, 4))
     sc.pl.violin(rna, 'log2FC', groupby='celltype', show=False, ax=ax, rotation=90)
-    ax.set_title(f'{gene} expression change')
+    ax.set_title(f'{max_gene if use_max_gene else gene} expression change')
     ax.hlines(0, -1, len(celltypes), linestyles='dashed')
     fig.tight_layout()
     fig.canvas.draw()