anno plotting module anno.pl

Setting

set_default_plotstyle

Set the plotly template for the vampire package.

Copy Number Variation

waterfall	Create a waterfall plot for motif composition across samples.
waterfall_legend	Create a legend figure for the waterfall plot.
copy_number_violin	Plot copy-number distribution across sample groups as a violin plot.
copy_number_stacked_violin	Plot copy-number distributions for multiple motifs as stacked violins.

Motif Variation Pattern

logo	Plot the logo plot from anndata object.
motif_msa	Plot motif alignment waterfall with variant pileup.

Motif Abundance

motif_abundance_heatmap	Plot a sample × motif abundance heatmap with hierarchical clustering and dendrograms.
motif_abundance_pca	Plot pairwise principal components from motif abundance PCA.
motif_abundance_pca_variance	Plot variance explained by each principal component.

Haplotype Clustering

haplotype_distance_heatmap	Plot sample pairwise distance matrix from haplotype analysis.
haplotype_leiden_res_scan	Plot cluster evaluation curve based on resolution-based evaluation (from vp.anno.tl.haplotype_leiden_res_scan()).

Multi-track Genomic Visualization

tracksplot

Create a multi-track genomic plot with shared x-axis.

Basic Plot Utilities

logo_from_matrix	Plot the logo plot from 2D matrix, such as count matrix, frequency matrix and position weight matrix (PWM).
heatmap_from_matrix	Plot a clustered heatmap from an arbitrary numeric matrix.