Package index • phiper

All functions

compute_alpha(): Compute alpha diversity per sample / group across ranks
compute_alpha_significance(): Compute statistical significance of alpha diversity between groups
compute_capscale(): Constrained Ordination (db-rda / cap) on Distance Matrix
compute_delta(): Global Shift in Peptide-level Prevalence via Subject-level Permutation
compute_dispersion(): Test Homogeneity of Dispersion (Beta Dispersion)
compute_distance(): Compute Pairwise Sample Distances
compute_pcoa(): Principal Components Analysis (PCoA) on a Distance Matrix
compute_pcoa_feature_associations(): Compute Feature Associations to PCoA Vectors
compute_permanova(): PERMANOVA with Global and Post-hoc Tests on Beta Diversity
compute_pop(): Prevalence comparison by group (POP framework)
compute_tsne(): Compute t-SNE Embeddings for Sample Distances
deltaplot(): Delta-prevalence vs Pooled Prevalence
deltaplot_interactive(): Interactive Delta-prevalence vs Pooled Prevalence
ecdf_plot(): ECDF of Per-peptide Prevalences for Two Groups
ecdf_plot_interactive(): ECDF of Per-peptide Prevalence for Two Groups
forestplot(): Forest Plot of Top/Bottom Raw Stouffer T by Rank
forestplot_interactive(): Interactive Forest Plot of Top/Bottom DELTA/Stouffer Statistics
get_example_path(): Path to Example PhIP-Seq Datasets
load_example_data(): Load Example PhIP-Seq Dataset as <phip_data>
phip_palette: PHIP default colour palette
plot_alpha(): Plot alpha diversity (richness/Shannon/Simpson) from precomputed results
plot_alpha_interactive(): Plot alpha diversity (precomputed) — interactive (plotly)
plot_alpha_significance(): Visualise alpha diversity significance results
plot_cap(): Plot CAP/db-RDA Results (Constrained Ordination)
plot_dispersion(): Plot beta dispersion (distance to centroid)
plot_enrichment_counts(): Plot enrichment counts per group (and optional interaction)
plot_pcoa(): Plot Principal Coordinates Analysis (PCoA)
plot_scree(): Scree Plot for PCoA Eigenvalues
plot_tsne(): Plot t-SNE embeddings
scale_colour_phip() scale_color_phip(): Discrete colour scale using the PHIP palette
scale_fill_phip(): Discrete fill scale using the PHIP palette
scatter_interactive(): Interactive prevalence scatter for prevalence results
scatter_static(): Static scatterplot of percent1 vs percent2 from compute_pop()
theme_phip(): Theme theme_phip
volcano_interactive(): Interactive volcano plot (log2 ratio vs -log10 p)
volcano_static(): Static volcano plot (log2 ratio vs -log10 p)