Merge trunk (#25)

* Bump pyarrow from 13.0.0 to 14.0.1 in /requirements (#22) Bumps [pyarrow](https://github.com/apache/arrow) from 13.0.0 to 14.0.1. - [Commits](apache/arrow@go/v13.0.0...apache-arrow-14.0.1) --- updated-dependencies: - dependency-name: pyarrow dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Clean jump notebook (#21) * convert string to Path in reading benchmark data * simple jump notebook * fix perturbation column * separate filtering from data loading * fix median syntax * Bump pyarrow from 13.0.0 to 14.0.1 in /requirements (#22) (#23) Bumps [pyarrow](https://github.com/apache/arrow) from 13.0.0 to 14.0.1. - [Commits](apache/arrow@go/v13.0.0...apache-arrow-14.0.1) --- updated-dependencies: - dependency-name: pyarrow dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * add no scaling option to align_on_controls * update docstring and delete the jump metadata files * convert read_parquet function to lambda function --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
recursionpharma · Nov 14, 2023 · 7170154 · 7170154
1 parent 2eec6db
commit 7170154
Show file tree

Hide file tree

Showing 16 changed files with 274 additions and 1,602 deletions.
diff --git a/efaar_benchmarking/benchmarking.py b/efaar_benchmarking/benchmarking.py
@@ -44,7 +44,7 @@ def pert_stats(
 def benchmark(
     map_data: Bunch,
     benchmark_sources: list = cst.BENCHMARK_SOURCES,
-    pert_label_col: str = cst.PERT_LABEL_COL,
+    pert_label_col: str = cst.REPLOGLE_PERT_LABEL_COL,
     recall_thr_pairs: list = cst.RECALL_PERC_THRS,
     filter_on_pert_prints: bool = False,
     pert_pval_thr: float = cst.PERT_SIG_PVAL_THR,
@@ -78,15 +78,15 @@ def benchmark(
     """
 
     if not len(benchmark_sources) > 0 and all([src in benchmark_data_dir for src in benchmark_sources]):
-        AssertionError("Invalid benchmark source(s) provided.")
+        ValueError("Invalid benchmark source(s) provided.")
     md = map_data.metadata
     idx = (md[cst.PERT_SIG_PVAL_COL] <= pert_pval_thr) if filter_on_pert_prints else [True] * len(md)
     features = map_data.features[idx].set_index(md[idx][pert_label_col]).rename_axis(index=None)
     del map_data
     if not len(features) == len(set(features.index)):
-        AssertionError("Duplicate perturbation labels in the map.")
+        ValueError("Duplicate perturbation labels in the map.")
     if not len(features) >= min_req_entity_cnt:
-        AssertionError("Not enough entities in the map for benchmarking.")
+        ValueError("Not enough entities in the map for benchmarking.")
     print(len(features), "perturbations exist in the map.")
 
     metrics_lst = []
@@ -98,7 +98,9 @@ def benchmark(
         random_seed_str = f"{rs1}_{rs2}"
         null_cossim = generate_null_cossims(features, n_null_samples, rs1, rs2)
         for s in benchmark_sources:
-            query_cossim = generate_query_cossims(features, get_benchmark_relationships(benchmark_data_dir, s))
+            rels = get_benchmark_relationships(benchmark_data_dir, s)
+            print(len(rels), "relationships exist in the benchmark source.")
+            query_cossim = generate_query_cossims(features, rels)
             if len(query_cossim) > 0:
                 metrics_lst.append(
                     convert_metrics_to_df(

diff --git a/efaar_benchmarking/constants.py b/efaar_benchmarking/constants.py
@@ -2,12 +2,16 @@
 
 BENCHMARK_DATA_DIR = str(resources.files("efaar_benchmarking").joinpath("benchmark_annotations"))
 BENCHMARK_SOURCES = ["Reactome", "HuMAP", "CORUM", "SIGNOR", "StringDB"]
-PERT_LABEL_COL = "gene"
-CONTROL_PERT_LABEL = "non-targeting"
-PERT_SIG_PVAL_COL = "gene_pvalue"
-PERT_SIG_PVAL_THR = 0.01
 RECALL_PERC_THRS = [(0.05, 0.95), (0.1, 0.9)]
 RANDOM_SEED = 42
 RANDOM_COUNT = 3
 N_NULL_SAMPLES = 5000
 MIN_REQ_ENT_CNT = 20
+PERT_SIG_PVAL_COL = "gene_pvalue"
+PERT_SIG_PVAL_THR = 0.01
+CONTROL_PERT_LABEL = "non-targeting"
+REPLOGLE_PERT_LABEL_COL = "gene"
+REPLOGLE_BATCH_COL = "gem_group"
+JUMP_PERT_LABEL_COL = "Metadata_Symbol"
+JUMP_PLATE_COL = "Metadata_Plate"
+JUMP_BATCH_COL = "Metadata_Batch"
diff --git a/efaar_benchmarking/data_loading.py b/efaar_benchmarking/data_loading.py
@@ -1,17 +1,95 @@
 import os
+import shutil
+import tempfile
+import zipfile
+from concurrent.futures import ThreadPoolExecutor, as_completed
 
 import numpy as np
+import pandas as pd
 import scanpy as sc
 import wget
 
 
-def load_replogle(gene_type, data_type, data_path="data/"):
+def load_cpg16_crispr(data_path: str = "data/") -> tuple[pd.DataFrame, pd.DataFrame]:
     """
-    Load Replogle et al. 2020 single-cell RNA-seq data for K562 cells.
+    Load and return the JUMP-CP (cpg0016) CRISPR dataset.
+    The metadata is downloaded from here:
+        https://zenodo.org/records/7661296/files/jump-cellpainting/metadata-v0.5.0.zip?download=1
+    The cellprofiler features are downloaded from here:
+        https://cellpainting-gallery.s3.amazonaws.com/index.html#cpg0016-jump/
+    We read the metadata first, filter it to CRISPR plates, and download the features for these plates only.
+
+    Parameters:
+    data_path (str): Path to the directory containing the dataset files.
+
+    Returns:
+    tuple[pd.DataFrame, pd.DataFrame]: A tuple containing two DataFrames:
+        - features: A DataFrame containing the CRISPR dataset features.
+        - metadata: A DataFrame containing the CRISPR dataset metadata.
+    """
+    metadata_source_path = "https://zenodo.org/records/7661296/files/jump-cellpainting/datasets-v0.5.0.zip?download=1"
+    plate_file_name = "plate.csv.gz"
+    well_file_name = "well.csv.gz"
+    crispr_file_name = "crispr.csv.gz"
+    plate_file_path = os.path.join(data_path, plate_file_name)
+    well_file_path = os.path.join(data_path, well_file_name)
+    crispr_file_path = os.path.join(data_path, crispr_file_name)
+    if not (os.path.exists(plate_file_path) and os.path.exists(well_file_path) and os.path.exists(crispr_file_path)):
+        path_to_zip_file = data_path + "tmp.zip"
+        wget.download(metadata_source_path, path_to_zip_file)
+        with zipfile.ZipFile(path_to_zip_file, "r") as zip_ref:
+            for name in zip_ref.namelist():
+                if name.endswith(plate_file_name) or name.endswith(well_file_name) or name.endswith(crispr_file_name):
+                    with tempfile.TemporaryDirectory() as temp_dir:
+                        zip_ref.extract(name, temp_dir)
+                        shutil.move(os.path.join(temp_dir, name), os.path.join(data_path, os.path.basename(name)))
+        os.remove(path_to_zip_file)
+
+    plates = pd.read_csv(plate_file_path)
+    crispr_plates = plates.query("Metadata_PlateType=='CRISPR'")
+    wells = pd.read_csv(well_file_path)
+    well_plate = wells.merge(crispr_plates, on=["Metadata_Source", "Metadata_Plate"])
+    crispr = pd.read_csv(crispr_file_path)
+    metadata = well_plate.merge(crispr, on="Metadata_JCP2022")
+
+    cp_feature_source_formatter = (
+        "s3://cellpainting-gallery/cpg0016-jump/"
+        "{Metadata_Source}/workspace/profiles/"
+        "{Metadata_Batch}/{Metadata_Plate}/{Metadata_Plate}.parquet"
+    )
+
+    features_file_path = os.path.join(data_path, "cpg_features.parquet")
+    if not os.path.exists(features_file_path):
+        cripsr_plates = metadata[
+            ["Metadata_Source", "Metadata_Batch", "Metadata_Plate", "Metadata_PlateType"]
+        ].drop_duplicates()
+        features = []
+        with ThreadPoolExecutor(max_workers=10) as executer:
+            future_to_plate = {
+                executer.submit(
+                    lambda path: pd.read_parquet(path, storage_options={"anon": True}),
+                    cp_feature_source_formatter.format(**row.to_dict()),
+                ): cp_feature_source_formatter.format(**row.to_dict())
+                for _, row in cripsr_plates.iterrows()
+            }
+            for future in as_completed(future_to_plate):
+                features.append(future.result())
+        pd.concat(features).to_parquet(features_file_path)
+    features = pd.read_parquet(features_file_path).dropna(axis=1)
+    return features, metadata
+
+
+def load_replogle(gene_type: str, data_type: str, data_path: str = "data/") -> sc.AnnData:
+    """
+    Load Replogle et al. 2022 single-cell RNA-seq data for K562 cells  published here:
+        https://pubmed.ncbi.nlm.nih.gov/35688146/
+    Four types of K562 data and downloaded using the links at:
+        plus.figshare.com/articles/dataset/_Mapping_information-rich_genotype-phenotype_landscapes_with_genome-scale_Perturb-seq_Replogle_et_al_2022_processed_Perturb-seq_datasets/20029387
 
     Parameters:
     gene_type (str): Type of genes to load. Must be either 'essential' or 'genome_wide'.
     data_type (str): Type of data to load. Must be either 'raw' or 'normalized'.
+        Normalized means Z-normalized by gemgroup.
     data_path (str): Path to the directory where the data will be downloaded and saved.
 
     Returns:

diff --git a/efaar_benchmarking/efaar.py b/efaar_benchmarking/efaar.py
@@ -1,75 +1,139 @@
+from typing import Optional
+
 import numpy as np
 import pandas as pd
 import scanpy as sc
 from scvi.model import SCVI
+from sklearn.covariance import EllipticEnvelope
+from sklearn.decomposition import PCA
+from sklearn.preprocessing import StandardScaler
 from sklearn.utils import Bunch
 
 import efaar_benchmarking.constants as cst
 
 
-def embed_by_scvi(adata, batch_key="gem_group", n_latent=128, n_hidden=256):
+def embed_by_scvi_anndata(adata, batch_col=cst.REPLOGLE_BATCH_COL, n_latent=128, n_hidden=256) -> np.ndarray:
     """
-    Embeds the input AnnData object using scVI.
+    Embed the input AnnData object using scVI.
 
-    Parameters:
-    adata (anndata.AnnData): The AnnData object to be embedded.
-    batch_key (str): The batch key in the AnnData object. Default is "gem_group".
-    n_latent (int): The number of latent dimensions. Default is 128.
-    n_hidden (int): The number of hidden dimensions. Default is 256.
+    Args:
+        adata (anndata.AnnData): The AnnData object to be embedded.
+        batch_col (str): The batch key in the AnnData object. Default is "gem_group".
+        n_latent (int): The number of latent dimensions. Default is 128.
+        n_hidden (int): The number of hidden dimensions. Default is 256.
 
     Returns:
-    None
+        numpy.ndarray: Embedding of the input data using scVI.
     """
-    SCVI.setup_anndata(adata, batch_key=batch_key)
+    SCVI.setup_anndata(adata, batch_key=batch_col)
     vae = SCVI(adata, n_hidden=n_hidden, n_latent=n_latent)
     vae.train(use_gpu=True)
     return vae.get_latent_representation()
 
 
-def embed_by_pca(adata, n_latent=100):
+def embed_by_pca_anndata(adata, n_latent=100) -> np.ndarray:
     """
-    Embeds the input data using PCA.
+    Embed the input data using principal component analysis (PCA).
+    Note that the data is centered by the `pca` function prior to PCA transformation.
 
-    Parameters:
-    adata (AnnData): Annotated data matrix.
-    n_latent (int): Number of principal components to use.
+    Args:
+        adata (AnnData): Annotated data matrix.
+        n_latent (int): Number of principal components to use.
 
     Returns:
-    numpy.ndarray: Embedding of the input data using PCA.
+        numpy.ndarray: Embedding of the input data using PCA.
     """
     sc.pp.pca(adata, n_comps=n_latent)
     return adata.obsm["X_pca"]
 
 
-def align_by_centering(embeddings, metadata, control_key=cst.CONTROL_PERT_LABEL, pert_col=cst.PERT_LABEL_COL):
+def embed_align_by_pca(
+    features: np.ndarray,
+    metadata: pd.DataFrame = None,
+    variance_or_ncomp=100,
+    plate_col: Optional[str] = None,
+) -> np.ndarray:
+    """
+    Embed the input data using principal component analysis (PCA).
+    Note that we explicitly center & scale the data by plate before and after calling `PCA`.
+    Centering and scaling is done by plate if `plate_col` is not None, and on the whole data otherwise.
+    Note that `PCA` transformer also does mean-centering on the whole data prior to the PCA operation.
+    Args:
+        features (np.ndarray): Features to transform
+        metadata (pd.DataFrame): Metadata. Defaults to None.
+        variance_or_ncomp (float, optional): Variance or number of components to keep after PCA.
+            Defaults to 100 (n_components). If between 0 and 1, select the number of components such that
+            the amount of variance that needs to be explained is greater than the percentage specified.
+        plate_col (str, optional): Column name for plate metadata. Defaults to None.
+    Returns:
+        np.ndarray: Transformed data using PCA.
+    """
+
+    def centerscale(features, metadata, plate_col):
+        if plate_col is None:
+            features = StandardScaler().fit_transform(features)
+        else:
+            if metadata is None:
+                raise ValueError("metadata must be provided if plate_col is not None")
+            unq_plates = metadata[plate_col].unique()
+            for plate in unq_plates:
+                ind = metadata[plate_col] == plate
+                features[ind, :] = StandardScaler().fit_transform(features[ind, :])
+        return features
+
+    features = centerscale(features, metadata, plate_col)
+    features = PCA(variance_or_ncomp).fit_transform(features)
+    features = centerscale(features, metadata, plate_col)
+
+    return features
+
+
+def align_on_controls(
+    embeddings: np.ndarray,
+    metadata: pd.DataFrame,
+    scale: bool = True,
+    pert_col: str = cst.REPLOGLE_PERT_LABEL_COL,
+    control_key: str = cst.CONTROL_PERT_LABEL,
+) -> np.ndarray:
     """
-    Applies the centerscale method to align embeddings based on the centering perturbations in the metadata.
+    Center the embeddings by the control perturbation units in the metadata.
 
     Args:
         embeddings (numpy.ndarray): The embeddings to be aligned.
         metadata (pandas.DataFrame): The metadata containing information about the embeddings.
+        scale (bool): Whether to scale the embeddings besides centering. Defaults to True.
+        pert_col (str, optional): The column in the metadata containing perturbation information.
+            Defaults to cst.REPLOGLE_PERT_LABEL_COL.
         control_key (str, optional): The key for non-targeting controls in the metadata.
             Defaults to cst.CONTROL_PERT_LABEL.
-        pert_col (str, optional): The column in the metadata containing perturbation information.
-            Defaults to cst.PERT_LABEL_COL.
 
     Returns:
         numpy.ndarray: The aligned embeddings.
     """
-    ntc_idxs = np.where(metadata[pert_col].values == control_key)[0]
-    ntc_center = embeddings[ntc_idxs].mean(0)
-    return embeddings - ntc_center
-
-
-def aggregate_by_mean(embeddings, metadata, control_key=cst.CONTROL_PERT_LABEL, pert_col=cst.PERT_LABEL_COL):
+    ss = StandardScaler() if scale else StandardScaler(with_std=False)
+    ss.fit(embeddings[metadata[pert_col].values == control_key])
+    return ss.transform(embeddings)
+
+
+def aggregate(
+    embeddings: np.ndarray,
+    metadata: pd.DataFrame,
+    pert_col: str = cst.REPLOGLE_PERT_LABEL_COL,
+    control_key: str = cst.CONTROL_PERT_LABEL,
+    method="mean",
+) -> Bunch[pd.DataFrame, pd.DataFrame]:
     """
-    Applies the mean aggregation to aggregate replicate embeddings for each perturbation.
+    Apply the mean or median aggregation to replicate embeddings for each perturbation.
 
     Args:
         embeddings (numpy.ndarray): The embeddings to be aggregated.
         metadata (pandas.DataFrame): The metadata containing information about the embeddings.
-        control_key (str, optional): The key for non-targeting controls in the metadata. Defaults to "non-targeting".
-        PERT_COL (str, optional): The column in the metadata containing perturbation information. Defaults to "gene".
+        pert_col (str, optional): The column in the metadata containing perturbation information.
+            Defaults to cst.REPLOGLE_PERT_LABEL_COL.
+        control_key (str, optional): The key for non-targeting controls in the metadata.
+            Defaults to cst.CONTROL_PERT_LABEL.
+        method (str, optional): The aggregation method to use. Must be either "mean" or "median".
+            Defaults to "mean".
 
     Returns:
         Bunch: A named tuple containing two pandas DataFrames:
@@ -81,5 +145,50 @@ def aggregate_by_mean(embeddings, metadata, control_key=cst.CONTROL_PERT_LABEL,
     final_embeddings = np.zeros((len(unique_perts), embeddings.shape[1]))
     for i, pert in enumerate(unique_perts):
         idxs = np.where(metadata[pert_col].values == pert)[0]
-        final_embeddings[i, :] = embeddings[idxs, :].mean(0)
+        if method == "mean":
+            final_embeddings[i, :] = np.mean(embeddings[idxs, :], axis=0)
+        elif method == "median":
+            final_embeddings[i, :] = np.median(embeddings[idxs, :], axis=0)
+        else:
+            raise ValueError(f"Invalid aggregation method: {method}")
     return Bunch(features=pd.DataFrame(final_embeddings), metadata=pd.DataFrame.from_dict({pert_col: unique_perts}))
+
+
+def filter_cpg16_crispr(
+    features: pd.DataFrame,
+    metadata: pd.DataFrame,
+    filter_by_intensity: bool = True,
+    filter_by_cell_count: bool = True,
+    drop_image_cols: bool = True,
+) -> tuple[pd.DataFrame, pd.DataFrame]:
+    """
+    Filter the given features and metadata dataframes based on various criteria.
+
+    Args:
+        features (pd.DataFrame): A dataframe containing the features to filter.
+        metadata (pd.DataFrame): A dataframe containing the metadata to filter.
+        filter_by_intensity (bool, optional): Whether to filter by intensity. Defaults to True.
+        filter_by_cell_count (bool, optional): Whether to filter by cell count. Defaults to True.
+        drop_image_cols (bool, optional): Whether to drop image columns. Defaults to True.
+
+    Returns:
+        Tuple[pd.DataFrame, pd.DataFrame]: A tuple containing the filtered features and metadata dataframes.
+    """
+    if filter_by_intensity:
+        features = features.loc[
+            EllipticEnvelope(contamination=0.01, random_state=42).fit_predict(
+                features[[col for col in features.columns if "ImageQuality_MeanIntensity" in col]]
+            )
+            == 1
+        ]
+    if filter_by_cell_count:
+        mask = np.full(len(features), True)
+        for colname in ["Cytoplasm_Number_Object_Number", "Nuclei_Number_Object_Number"]:
+            mask = mask & (features[colname] >= 50) & (features[colname] <= 350)
+        features = features.loc[mask]
+    if drop_image_cols:
+        features = features.drop(columns=[col for col in features.columns if col.startswith("Image_")])
+
+    metadata_cols = metadata.columns
+    merged_data = metadata.merge(features, on=["Metadata_Source", "Metadata_Plate", "Metadata_Well"])
+    return merged_data.drop(columns=metadata_cols), merged_data[metadata_cols]
diff --git a/efaar_benchmarking/plotting.py b/efaar_benchmarking/plotting.py
@@ -49,7 +49,6 @@ def plot_recall(df):
         curr_ax.set_ylabel("Recall Value")
         curr_ax.set_xticks(range(len(x_values_orig)))
         curr_ax.set_xticklabels(x_values_orig, rotation=45)
-        curr_ax.set_ylim(0, 0.8)
 
     plt.tight_layout()
     plt.show()
diff --git a/notebooks/data/crispr.csv.gz b/notebooks/data/crispr.csv.gz
diff --git a/notebooks/data/plate.csv.gz b/notebooks/data/plate.csv.gz
diff --git a/notebooks/data/well.csv.gz b/notebooks/data/well.csv.gz