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Log transform data for infercnvpy #41

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merged 1 commit into from
May 11, 2024
Merged

Log transform data for infercnvpy #41

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19 changes: 17 additions & 2 deletions proxbias/scPerturb_processing_plotting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -196,7 +196,7 @@ def _load_and_process_data(filename: str, chromosome_info: Optional[pd.DataFrame
if not os.path.exists(destination_path):
source_path = f"https://zenodo.org/record/7416068/files/{filename}.h5ad?download=1"
wget.download(source_path, destination_path)
ad = scanpy.read_h5ad(destination_path)
ad = read_and_log_transform_h5ad_file(destination_path)
ad.var = ad.var.rename(columns={"start": "st", "end": "en"}).join(chromosome_info, how="left")
if filename.startswith("Adamson"):
ad.obs["gene"] = ad.obs.perturbation.apply(lambda x: x.split("_")[0]).fillna("")
Expand Down Expand Up @@ -529,6 +529,21 @@ def _get_perturbation_type(filename_short: str):
}[filename_short]


def read_and_log_transform_h5ad_file(filename: str) -> AnnData:
"""
Read and log-transform the specified h5ad single-cell perturb-seq file.

Args:
filename (str): The name of the dataset file to read and log-transform.

Returns:
AnnData: The log-transformed dataset as an AnnData object.
"""
ad = scanpy.read_h5ad(filename)
scanpy.pp.log1p(ad)
return ad


def plot_loss_for_selected_genes(
filenames: List[str],
chromosome_info: Optional[pd.DataFrame] = None,
Expand Down Expand Up @@ -567,7 +582,7 @@ def plot_loss_for_selected_genes(
sns.set(font_scale=1.7)
plt.rcParams["svg.fonttype"] = "none"
for filename in filenames:
ad = scanpy.read_h5ad(os.path.join(str(utils.constants.DATA_DIR), f"{filename}.h5ad"))
ad = read_and_log_transform_h5ad_file(os.path.join(str(utils.constants.DATA_DIR), f"{filename}.h5ad"))
filename_short = _get_short_filename(filename)
perts2check_df = allres[
(allres["Dataset"] == filename_short)
Expand Down
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