Plotting

Imaging

plotting.dynamic_histogram(df, column[, bins])	Plot a dynamic histogram with a threshold slider and count annotations.
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 correlation heatmap of the protein abundance for all samples in adata.
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_obs[, ...])	Generates a dual-axis plot with boxplots and stripplots for two features grouped by a specified feature key.
plotting.histogram_w_imputation(...[, ...])	Plot histograms for each sample showing raw and imputed values before and after imputation.
plotting.pca_loadings(adata[, top, n_pcs, ...])	Plot PCA protein loadings for the top features in the first two principal components.
plotting.pca(adata[, color, group_colors, ...])	Plot PCA of samples in an AnnData object using Plotly.
plotting.rankplot(adata, adata_obs_key, groups)	Plot a rank plot of average protein abundance in an AnnData object.
plotting.upset(adata, groupby[, threshold, ...])	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.