index.rst

episcanpy

API

Import epiScanpy's high-level API as:

import episcanpy.api as epi

Count Matrices: CT

Loading data, loading annotations, building count matrices, filtering of lowly covered methylation variables. Filtering of lowly covered cells.

Building count matrices

Quickly build a count matrix from tsv/tbi file.

episcanpy.api

ct.bld_mtx_fly

Load features

In order to build a count matrix for either methylation or open chromatin data, loading the segmentation of the genome of interest or the set of features of interest is a prerequirement.

ct.load_features ct.make_windows ct.size_feature_norm ct.plot_size_features ct.name_features

Reading methylation file

Functions to read methylation files, extract methylation and buildthe count matrices:

ct.build_count_mtx ct.read_cyt_summary ct.load_met_noimput

Reading open chromatin(ATAC) file

ATAC-seq specific functions to build count matrices and load data:

ct.bld_mtx_fly ct.save_sparse_mtx

General functions

Functions non -omic specific:

ct.save_sparse_mtx

Preprocessing: PP

Imputing missing data (methylation), filtering lowly covered cells or variables, correction for batch effect.

; pp.snap2anndata pp.coverage_cells pp.commonness_features pp.correlation_pc pp.coverage_features pp.density_features pp.select_var_feature pp.cal_var pp.variability_features pp.binarize pp.lazy pp.load_metadata pp.read_ATAC_10x pp.filter_cells pp.filter_features pp.normalize_total pp.pca pp.normalize_per_cell pp.regress_out pp.subsample pp.downsample_counts pp.neighbors pp.sparse pp.log1p pp.sparse

Methylation matrices

Methylation specific count matrices.

pp.imputation_met pp.load_met_noimput pp.readandimputematrix

Tools: TL

tl.rank_features

tl.lazy

tl.load_markers tl.identify_cluster

tl.top_feature_genes tl.var_features_to_genes ; tl.find_genes_in_features tl.geneactivity

tl.diffmap tl.draw_graph tl.tsne tl.umap tl.dpt

tl.louvain tl.leiden tl.kmeans tl.hc tl.getNClusters tl.dendogram

tl.ARI tl.AMI tl.homogeneity tl.silhouette

Plotting: PL

The plotting module episcanpy.plotting largely parallels the tl.* and a few of the pp.* functions. For most tools and for some preprocessing functions, you'll find a plotting function with the same name.

pl.pca pl.pca_loadings pl.pca_overview pl.pca_variance_ratio

pl.tsne pl.umap pl.diffmap pl.draw_graph

pl.rank_feat_groups pl.rank_feat_groups_violin pl.rank_feat_groups_dotplot pl.rank_feat_groups_stacked_violin pl.rank_feat_groups_matrixplot pl.rank_feat_groups_heatmap pl.rank_feat_groups_tracksplot pl.cal_var

pl.violin pl.scatter pl.ranking pl.clustermap pl.stacked_violin pl.heatmap pl.dotplot pl.matrixplot pl.tracksplot pl.dendrogram pl.correlation_matrix

pl.prct_overlap pl.overlap_heatmap pl.cluster_composition pl.silhouette pl.silhouette_tot

pl.cal_var pl.variability_features