API reference¶

This page is generated from the docstrings of every public symbol in cycombinepy. Click through to each function for the full parameter list, return type, and source link.

Preprocessing¶

`transform_asinh`	Asinh-transform marker columns of `adata` with an optional derandomization step.
`normalize`	Batch-wise normalize marker columns of `adata`.

Clustering¶

create_som

Train a FlowSOM on the marker columns of adata and store cluster labels.

Correction¶

`batch_correct`	Run normalization, SOM clustering, and per-cluster ComBat.
`correct_data`	Per-cluster ComBat batch correction.
`CombatCorrectionError`	Raised when per-cluster ComBat fails under `error_policy='raise'`.
`ConfoundedDesignError`	Raised when covariates are confounded under `confound_policy='raise'`.

Correction reports and constants¶

`CORRECTED_LAYER`	str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str
`CORRECTION_REPORT_UNS_KEY`	str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str
`CORRECTION_REPORT_SCHEMA_VERSION`	str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str

Evaluation¶

`compute_emd`	Per (cluster, marker, batch-pair) 1-D Earth Mover's distance.
`evaluate_emd`	Join uncorrected vs corrected EMD and compute percent reduction.
`compute_mad`	Per (cluster, marker, batch) Median Absolute Deviation.
`evaluate_mad`	Join uncorrected vs corrected MAD and compute percent reduction.

Detection¶

`detect_batch_effect`	Extended batch-effect diagnostic: express output plus UMAP and MAD.
`detect_batch_effect_express`	Quick 3-panel batch-effect summary (EMD heatmap, density, MDS).

Utilities¶

`get_markers`	Return var_names that are not in the non-markers blacklist (case-insensitive).
`check_confound`	Return True if `batch` is confounded with `mod`.

I/O¶

read_fcs_dir

Read all FCS files in data_dir into a single AnnData.

Plotting¶

`plot_density`	Per-marker density plot colored by batch.
`plot_dimred`	Thin wrapper around `scanpy.pl.umap` / `scanpy.pl.pca`.
`plot_emd_heatmap`	Heatmap of mean EMD per (cluster, marker) from `compute_emd()` output.

Advanced evaluation¶

scib_metrics

Run selected scib-metrics batch-correction metrics on an AnnData.