ctheodoris davidjwen commited on
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Upload in_silico_perturber_stats.py (#313)

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- Upload in_silico_perturber_stats.py (bde1f23f2712777472216e49c30b21cdcb4543ee)


Co-authored-by: David Wen <[email protected]>

geneformer/in_silico_perturber_stats.py CHANGED
@@ -192,16 +192,27 @@ def get_impact_component(test_value, gaussian_mixture_model):
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  # aggregate data for single perturbation in multiple cells
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- def isp_aggregate_grouped_perturb(cos_sims_df, dict_list):
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- names = ["Cosine_shift"]
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- cos_sims_full_df = pd.DataFrame(columns=names)
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- cos_shift_data = []
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- token = cos_sims_df["Gene"][0]
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- for dict_i in dict_list:
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- cos_shift_data += dict_i.get((token, "cell_emb"), [])
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- cos_sims_full_df["Cosine_shift"] = cos_shift_data
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- return cos_sims_full_df
 
 
 
 
 
 
 
 
 
 
 
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  def find(variable, x):
@@ -1017,8 +1028,8 @@ class InSilicoPerturberStats:
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  cos_sims_df_initial, dict_list, self.combos, self.anchor_token
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  )
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- elif self.mode == "aggregate_data":
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- cos_sims_df = isp_aggregate_grouped_perturb(cos_sims_df_initial, dict_list)
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  elif self.mode == "aggregate_gene_shifts":
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  cos_sims_df = isp_aggregate_gene_shifts(
 
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  # aggregate data for single perturbation in multiple cells
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+ def isp_aggregate_grouped_perturb(cos_sims_df, dict_list, genes_perturbed):
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+ names = ["Cosine_shift", "Gene"]
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+ cos_sims_full_dfs = []
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+
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+ gene_ids_df = cos_sims_df.loc[np.isin(cos_sims_df["Ensembl_ID"], genes_perturbed), :]
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+ tokens = gene_ids_df["Gene"]
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+ symbols = gene_ids_df["Gene_name"]
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+
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+ for token, symbol in zip(tokens, symbols):
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+ cos_shift_data = []
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+ for dict_i in dict_list:
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+ cos_shift_data += dict_i.get((token, "cell_emb"), [])
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+
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+ df = pd.DataFrame(columns=names)
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+ df["Cosine_shift"] = cos_shift_data
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+ df["Gene"] = symbol
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+ cos_sims_full_dfs.append(df)
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+
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+
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+ return pd.concat(cos_sims_full_dfs)
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  def find(variable, x):
 
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  cos_sims_df_initial, dict_list, self.combos, self.anchor_token
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  )
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+ elif self.mode == "aggregate_data":
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+ cos_sims_df = isp_aggregate_grouped_perturb(cos_sims_df_initial, dict_list, self.genes_perturbed)
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  elif self.mode == "aggregate_gene_shifts":
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  cos_sims_df = isp_aggregate_gene_shifts(