Plotting: pl

This module provides visualization functions for proteomics data.

Note

Many of Scanpy’s plotting functions can be used directly with grassp AnnData objects. If you are looking for a specific plot, check whether it is already implemented in Scanpy.

Preprocessing

pl.highly_variable_proteins	Mean–variance relationship for protein expression.
pl.bait_volcano_plots	Volcano plots for enrichment of pull-down baits.
pl.protein_clustermap	Clustered heat-map of pair-wise protein distances.
pl.sample_heatmap	Correlation heat-map between samples (columns of data).

Integration

pl.aligned_umap	Side-by-side visualisation of aligned UMAP embeddings.
pl.remodeling_score	Visualise the distribution of protein remodeling scores.
pl.remodeling_sankey	Sankey diagram of cluster re-assignment between two conditions.
pl.mr_plot	MR-plot for simultaneous visualisation of M and R scores.

Clustering

pl.qsep_heatmap	Plot QSep cluster distance heatmap.
pl.qsep_boxplot	Plot QSep cluster distances as boxplots.
pl.tagm_map_contours	Plot posterior density contours of TAGM components in embedding space.
pl.tagm_map_pca_ellipses	Visualize TAGM component covariance as ellipses in PCA space.
pl.knn_violin	Violin plot of KNN annotation.

Ternary

pl.ternary

Scatter plot of 3-part compositions in a ternary diagram.