dylanplummer commited on
Commit
44a3abc
·
1 Parent(s): 28c4be5

fix celltype heatmap gen

Browse files
Files changed (1) hide show
  1. app.py +4 -4
app.py CHANGED
@@ -41,9 +41,9 @@ graph_file = hf_hub_download(repo_id="dylanplummer/islet-epigenome", filename=f"
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  rna_file = unzip(rna_file)
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  hic_file = unzip(hic_file)
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- celltypes = ['Alpha', 'Beta', 'Delta', 'PP', 'Acinar', 'Duct', 'PSC', 'Endothelial']
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  coolers = []
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- for celltype in celltypes:
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  cooler_file = hf_hub_download(repo_id="dylanplummer/islet-epigenome", filename=f"pseudobulk_coolers/{celltype}_50kb.cool", repo_type="dataset", token=os.environ['DATASET_SECRET'])
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  coolers.append(cooler.Cooler(cooler_file))
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  beta_cooler = coolers[1]
@@ -206,7 +206,7 @@ def get_heatmap(celltype, gene, locus1, locus2, heatmap_range):
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  def get_heatmaps(gene, locus1, locus2, heatmap_range):
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  res = []
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- for celltype in celltypes:
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  res.append(get_heatmap(celltype, gene, locus1, locus2, heatmap_range))
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  alpha, beta, delta, pp, acinar, duct, psc, endothelial = res
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  return alpha, beta, delta, pp, acinar, duct, psc, endothelial
@@ -341,7 +341,7 @@ with gr.Blocks(theme='WeixuanYuan/Soft_dark') as demo:
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  heatmap_size = gr.Slider(label="Heatmap Range", info="kb range aroung input gene locus to expand", minimum=50, maximum=30000, value=2000)
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  with gr.Row():
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  out_heatmaps = []
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- for celltype, c in zip(celltypes, coolers):
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  out_heatmaps.append(gr.Image(label=celltype, elem_id=f'out-heatmap-{celltype}', scale=1))
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  with gr.Row():
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  heatmap_button = gr.Button(value="Generate Heatmaps", elem_id='heatmap-button', scale=1)
 
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  rna_file = unzip(rna_file)
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  hic_file = unzip(hic_file)
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+ cooler_celltypes = ['Alpha', 'Beta', 'Delta', 'PP', 'Acinar', 'Duct', 'PSC', 'Endothelial']
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  coolers = []
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+ for celltype in cooler_celltypes:
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  cooler_file = hf_hub_download(repo_id="dylanplummer/islet-epigenome", filename=f"pseudobulk_coolers/{celltype}_50kb.cool", repo_type="dataset", token=os.environ['DATASET_SECRET'])
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  coolers.append(cooler.Cooler(cooler_file))
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  beta_cooler = coolers[1]
 
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  def get_heatmaps(gene, locus1, locus2, heatmap_range):
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  res = []
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+ for celltype in cooler_celltypes:
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  res.append(get_heatmap(celltype, gene, locus1, locus2, heatmap_range))
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  alpha, beta, delta, pp, acinar, duct, psc, endothelial = res
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  return alpha, beta, delta, pp, acinar, duct, psc, endothelial
 
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  heatmap_size = gr.Slider(label="Heatmap Range", info="kb range aroung input gene locus to expand", minimum=50, maximum=30000, value=2000)
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  with gr.Row():
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  out_heatmaps = []
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+ for celltype, c in zip(cooler_celltypes, coolers):
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  out_heatmaps.append(gr.Image(label=celltype, elem_id=f'out-heatmap-{celltype}', scale=1))
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  with gr.Row():
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  heatmap_button = gr.Button(value="Generate Heatmaps", elem_id='heatmap-button', scale=1)