update violins

app.py

@@ -173,6 +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
     
     fig = sc.pl.umap(rna, 
                      color=['celltype', 'log2FC'], 
@@ -193,21 +194,32 @@ def perturb(gene, locus1, locus2):
     # convert from argb to rgba
     image_from_plot = image_from_plot[:, :, [1, 2, 3, 0]]
 
-    fig, ax = plt.subplots(figsize=(6, 6))
-    sc.pl.violin(rna, gene, groupby='celltype', show=False, ax=ax)
+    fig, ax = plt.subplots(figsize=(6, 3))
+    sc.pl.violin(rna, gene, groupby='celltype', layer='counts', show=False, ax=ax)
+    ax.set_title(f'Normal {gene} expression')
     fig.canvas.draw()
     violin_img = np.frombuffer(fig.canvas.tostring_argb(), dtype=np.uint8)
     violin_img = violin_img.reshape(fig.canvas.get_width_height()[::-1] + (4,))
     violin_img = violin_img[:, :, [1, 2, 3, 0]]
 
-    fig, ax = plt.subplots(figsize=(6, 6))
+    fig, ax = plt.subplots(figsize=(6, 3))
+    sc.pl.violin(rna, gene, groupby='celltype', layer='new_counts', 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)
+    violin_img_new = violin_img_new.reshape(fig.canvas.get_width_height()[::-1] + (4,))
+    violin_img_new = violin_img_new[:, :, [1, 2, 3, 0]]
+
+    fig, ax = plt.subplots(figsize=(6, 3))
     sc.pl.violin(rna, 'log2FC', groupby='celltype', show=False, ax=ax)
+    ax.set_title(f'{gene} expression change')
+    ax.hlines(0, -1, len(celltypes), linestyles='dashed')
     fig.canvas.draw()
     violin_img_fc = np.frombuffer(fig.canvas.tostring_argb(), dtype=np.uint8)
     violin_img_fc = violin_img_fc.reshape(fig.canvas.get_width_height()[::-1] + (4,))
     violin_img_fc = violin_img_fc[:, :, [1, 2, 3, 0]]
 
-    return image_from_plot, violin_img, violin_img_fc
+    return image_from_plot, violin_img, violin_img_new, violin_img_fc
 
 
 
@@ -223,11 +235,12 @@ with gr.Blocks(theme='WeixuanYuan/Soft_dark') as demo:
         out_img = gr.Image(elem_id='out-img', scale=1)
     with gr.Row():
         out_violin = gr.Image(elem_id='out-violin', scale=1)
+        out_violin_new = gr.Image(elem_id='out-violin-new', scale=1)
         out_violin_fc = gr.Image(elem_id='out-violin-fc', scale=1)
         #out_plot = gr.Plot(elem_id='out-plot', scale=1)
 
     inputs = [in_locus, anchor1, anchor2]
-    outputs = [out_img, out_violin, out_violin_fc]
+    outputs = [out_img, out_violin, out_violin_new, out_violin_fc]
 
     gr.Examples(examples=[['INS', 'chr11:2,289,895', 'chr11:2,298,840'],
                           ['INS', 'INS', 'IGF1'],
@@ -239,7 +252,7 @@ with gr.Blocks(theme='WeixuanYuan/Soft_dark') as demo:
                 inputs=inputs,
                 outputs=outputs,
                 fn=perturb, cache_examples=os.getenv('SYSTEM') == 'spaces')
-    run_button.click(perturb, [in_locus, anchor1, anchor2], outputs=outputs)
+    run_button.click(perturb, inputs, outputs=outputs)
 
 
 if __name__ == "__main__":