Plotting

Imaging

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

Proteomics

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