Plotting: pl

This module provides visualization functions for proteomics data.

Note

Many of scanpy’s plotting functions can be directly used with grassp AnnData objects. So if you are looking for a specific plot, it is worth checking if it is already implemented in scanpy.

Preprocessing

pl.highly_variable_proteins	Plot dispersions versus means for highly variable proteins.
pl.bait_volcano_plots	Create volcano plots for bait enrichment analysis.
pl.protein_clustermap	Create a clustered heatmap of protein distances with annotations.

Integration

pl.aligned_umap	Plot aligned UMAP embeddings for two datasets.
pl.remodeling_score	Plot remodeling score distribution.
pl.remodeling_sankey	Plot a Sankey diagram showing protein transitions between clusters.

Clustering

pl.tagm_map_contours	Plot the TAGM map of the adata object.
pl.tagm_map_pca_ellipses	Plot the PCA ellipses of the TAGM map of the adata object.