scanpy.pp.highly_variable_genes

scanpy.pp.highly_variable_genes(adata, layer=None, n_top_genes=None, min_disp=0.5, max_disp=inf, min_mean=0.0125, max_mean=3, span=0.3, n_bins=20, flavor='seurat', subset=False, inplace=True, batch_key=None, check_values=True)

Annotate highly variable genes [Satija15] [Zheng17] [Stuart19].

Expects logarithmized data, except when flavor='seurat_v3', in which count data is expected.

Depending on flavor, this reproduces the R-implementations of Seurat [Satija15], Cell Ranger [Zheng17], and Seurat v3 [Stuart19].

For the dispersion-based methods ([Satija15] and [Zheng17]), the normalized dispersion is obtained by scaling with the mean and standard deviation of the dispersions for genes falling into a given bin for mean expression of genes. This means that for each bin of mean expression, highly variable genes are selected.

For [Stuart19], a normalized variance for each gene is computed. First, the data are standardized (i.e., z-score normalization per feature) with a regularized standard deviation. Next, the normalized variance is computed as the variance of each gene after the transformation. Genes are ranked by the normalized variance.

See also scanpy.experimental.pp._highly_variable_genes for additional flavours (e.g. Pearson residuals).

Parameters:

adata : AnnData

The annotated data matrix of shape n_obs × n_vars. Rows correspond to cells and columns to genes.

layer : str | None (default: None)

If provided, use adata.layers[layer] for expression values instead of adata.X.

n_top_genes : int | None (default: None)

Number of highly-variable genes to keep. Mandatory if flavor='seurat_v3'.

min_mean : float | None (default: 0.0125)

If n_top_genes unequals None, this and all other cutoffs for the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'.

max_mean : float | None (default: 3)

If n_top_genes unequals None, this and all other cutoffs for the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'.

min_disp : float | None (default: 0.5)

If n_top_genes unequals None, this and all other cutoffs for the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'.

max_disp : float | None (default: inf)

If n_top_genes unequals None, this and all other cutoffs for the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'.

span : float (default: 0.3)

The fraction of the data (cells) used when estimating the variance in the loess model fit if flavor='seurat_v3'.

n_bins : int (default: 20)

Number of bins for binning the mean gene expression. Normalization is done with respect to each bin. If just a single gene falls into a bin, the normalized dispersion is artificially set to 1. You’ll be informed about this if you set settings.verbosity = 4.

flavor : Literal[‘seurat’, ‘cell_ranger’, ‘seurat_v3’] (default: 'seurat')

Choose the flavor for identifying highly variable genes. For the dispersion based methods in their default workflows, Seurat passes the cutoffs whereas Cell Ranger passes n_top_genes.

subset : bool (default: False)

Inplace subset to highly-variable genes if True otherwise merely indicate highly variable genes.

inplace : bool (default: True)

Whether to place calculated metrics in .var or return them.

batch_key : Optional[str] (default: None)

If specified, highly-variable genes are selected within each batch separately and merged. This simple process avoids the selection of batch-specific genes and acts as a lightweight batch correction method. For all flavors, genes are first sorted by how many batches they are a HVG. For dispersion-based flavors ties are broken by normalized dispersion. If flavor = 'seurat_v3', ties are broken by the median (across batches) rank based on within-batch normalized variance.

check_values : bool (default: True)

Check if counts in selected layer are integers. A Warning is returned if set to True. Only used if flavor='seurat_v3'.

Return type:

Optional[pd.DataFrame]

Returns:

: Depending on inplace returns calculated metrics (DataFrame) or updates .var with the following fields

highly_variablebool

boolean indicator of highly-variable genes

means

means per gene

dispersions

For dispersion-based flavors, dispersions per gene

dispersions_norm

For dispersion-based flavors, normalized dispersions per gene

variances

For flavor='seurat_v3', variance per gene

variances_norm

For flavor='seurat_v3', normalized variance per gene, averaged in the case of multiple batches

highly_variable_rankfloat

For flavor='seurat_v3', rank of the gene according to normalized variance, median rank in the case of multiple batches

highly_variable_nbatchesint

If batch_key is given, this denotes in how many batches genes are detected as HVG

highly_variable_intersectionbool

If batch_key is given, this denotes the genes that are highly variable in all batches

Notes

This function replaces filter_genes_dispersion().