Plotting

Imaging

pl.plot_graph_network(w, coords, threshold)	Plot the graph of connected nodes for a given threshold.
pl.stacked_barplot(df, phenotype_col, ...[, ...])	Plot a stacked barplot showing phenotype composition per RCN motif.

Proteomics

pl.abundance_histograms(adata[, n_cols, ...])	Plot histograms of protein abundance for each sample in adata.
pl.correlation_heatmap(adata[, ...])	Plot a clustered correlation heatmap of protein abundance for all samples in an AnnData object.
pl.coefficient_of_variation(adata, group_by)	Plot coefficient of variation (CV) for each group in AnnData.obs[group_by].
pl.density(adata, color_by[, color_dict, ...])	Plot density (KDE) plots of protein abundance grouped by a categorical variable in AnnData.obs.
pl.dual_axis_boxplots(adata, feature_1, ...)	Generates a dual-axis plot with boxplots and stripplots for two features.
pl.feature_comparison_boxplot(adata, ...[, ...])	Plots boxplots of feature expression from adata.X, comparing two groups.
pl.imputation_qc(adata[, unimputed_layer, ...])	Generate a quality control plot to visualize the effect of imputation.
pl.pca_loadings(adata[, top, n_pcs, ...])	Plot PCA protein loadings for the top features in the first two principal components.
pl.rankplot(adata, adata_obs_key[, ...])	Plot a rank plot of average protein abundance in an AnnData object.
pl.upset(adata, groupby[, ...])	Generate an UpSet plot from an AnnData object based on variable presence across groups.
pl.volcano(adata[, x, y, significant, FDR, ...])	Plot a volcano plot from an AnnData object.