pyrovelocity.data#

pyrovelocity.data.assign_colors(max_spliced, max_unspliced, minlim_s, minlim_u)[source]#
Return type:

List[str]

pyrovelocity.data.copy_raw_counts(adata)[source]#

Copy unspliced and spliced raw counts to adata.layers and adata.obs.

Parameters:

adata (anndata._core.anndata.AnnData) – AnnData object

Returns:

AnnData object with raw counts.

Return type:

anndata._core.anndata.AnnData

Examples

>>> from pyrovelocity.utils import generate_sample_data
>>> adata = generate_sample_data()
>>> copy_raw_counts(adata)
pyrovelocity.data.get_high_us_genes(adata, minlim_u=0, minlim_s=0, unspliced_layer='unspliced', spliced_layer='spliced')[source]#

Function to select genes that have spliced and unspliced counts above a certain threshold. Genes of which the maximum u and s count is above a set threshold are selected. Threshold varies per dataset and influences the numbers of genes that are selected.

Parameters:

  • adata – Annotated data matrix

  • minlim_u (int (default: 3)) – Threshold above which the maximum unspliced counts of a gene should fall to be included in the list of high US genes.

  • minlim_s (int (default: 3)) – Threshold above which the maximum spliced counts of a gene should fall to be included in the list of high US genes.

  • unspliced_layer (str (default: ‘unspliced’)) – Name of layer that contains the unspliced counts.

  • spliced_layer (str (default: ‘spliced’)) – Name of layer that contains the spliced counts.

pyrovelocity.data.get_thresh_histogram_title_from_path(path)[source]#
pyrovelocity.data.load_data(data='pancreas', top_n=2000, min_shared_counts=30, eps=1e-06, force=False, processed_path=None, process_cytotrace=False, use_sub=False, count_thres=0, thresh_histogram_path=None)[source]#

Preprocess data from scvelo.

Parameters:

  • data (str, optional) – data set name. Defaults to scvelo’s “pancreas” data set.

  • top_n (int, optional) – number of genes to retain. Defaults to 2000.

  • min_shared_counts (int, optional) – minimum shared counts. Defaults to 30.

  • eps (float, optional) – tolerance. Defaults to 1e-6.

  • force (bool, optional) – force reprocessing. Defaults to False.

  • processed_path (str, optional) – path to read/write processed AnnData. Defaults to None.

Returns:

processed AnnData object

Return type:

anndata._core.anndata.AnnData

pyrovelocity.data.load_larry(file_path='data/external/larry.h5ad')[source]#

In vitro Hemotopoiesis Larry datasets

Data from `CALEB WEINREB et al. (2020) <DOI: 10.1126/science.aaw3381>’ https://figshare.com/ndownloader/articles/20780344/versions/1

Return type:

Returns adata object

pyrovelocity.data.load_pbmc68k(data='pbmc68k', count_thres=0, thresh_histogram_path=None)[source]#
Return type:

AnnData

pyrovelocity.data.load_unipotent_larry(celltype='mono')[source]#

In vitro Hemotopoiesis Larry datasets Subset of Data from `CALEB WEINREB et al. (2020) <DOI: 10.1126/science.aaw3381>’ unipotent monocytes: https://figshare.com/ndownloader/files/37028572 unipotent neutrophils: https://figshare.com/ndownloader/files/37028575

Return type:

Returns adata object

pyrovelocity.data.plot_high_us_genes(adata, thresh_histogram_path, minlim_u=3, minlim_s=3, unspliced_layer='unspliced', spliced_layer='spliced')[source]#
Return type:

Optional[Figure]