ggpicrust2
Make 'PICRUSt2' Output Analysis and Visualization Easier

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ggpicrust2: Make 'PICRUSt2' Output Analysis and Visualization Easier
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API

API for ggpicrust2
Make 'PICRUSt2' Output Analysis and Visualization Easier

Global functions
.as_color_vector Man page Source code
.build_continuous_scale Man page Source code
.build_discrete_fill_for_direction Man page Source code
.build_heatmap_col_fun Man page Source code
.is_ggplot_scale Man page Source code
.onAttach Source code
.onLoad Source code
abundance_sample_columns Source code
abundance_to_numeric_matrix Source code
add_internal_metadata_column Source code
adjust_daa_p_values Source code
aggregate_taxa_contributions Man page Source code
align_metagenomeseq_fit_vector Source code
align_samples Source code
annotate_go_gsea Source code
annotate_gsea_from_lookup Source code
annotate_kegg_gsea Source code
annotate_metacyc_gsea Source code
annotate_pathways Source code
apply_taxonomy Source code
attach_abundance_stats Source code
build_annotation_label_map Source code
build_design_matrix Man page Source code
build_one_sided_formula Source code
build_two_sided_formula Source code
calculate_abundance_stats Man page Source code
calculate_lefser_kruskal_p_value Source code
calculate_log2_fold_change Man page Source code
calculate_pseudocount Man page Source code
calculate_rank_metric Man page Source code
calculate_smart_text_size Man page Source code
canonical_daa_group_pair Source code
canonicalize_daa_method_names Source code
choose_contribution_column Source code
clean_ko_abundance Source code
color_themes Man page
column_labels Source code
compare_daa_results Man page Source code
compare_gsea_daa Man page Source code
compare_metagenome_results Man page Source code
complete_contribution_grid Source code
complete_sample_function_totals Source code
compute_correlation_distance Man page Source code
compute_relative_abundance Source code
contribution_feature_levels Source code
contribution_metric_candidates Source code
create_comparison_count_plot Source code
create_dendrogram Man page Source code
create_empty_daa_result Source code
create_empty_gsea_result Source code
create_empty_plot Man page Source code
create_gradient_colors Man page Source code
create_heatmap_plot Man page Source code
create_legend_theme Man page Source code
create_network_plot Man page Source code
create_pathway_class_theme Man page Source code
create_progress_bar Source code
daa_annotated_results_df Man page
daa_results_df Man page
data_utils Man page
detect_contrib_feature_level Source code
ec_reference Man page
extract_compare_direction Source code
extract_linda_output_column Source code
extract_metagenomeseq_fit_values Source code
filter_contrib_by_features Source code
filter_gene_sets_to_ranked_universe Man page Source code
filter_kegg_reference_for_prokaryotes Source code
filter_kegg_reference_to_pathways Source code
find_sample_column Source code
format_daa_comparison_units Source code
format_linda_output Source code
format_metadata_row_labels Source code
format_pvalue_smart Man page Source code
generate_nested_colors Man page Source code
generate_sample_permutations Source code
get_available_themes Man page Source code
get_color_theme Man page Source code
get_kegg_with_cache Source code
get_significance_colors Man page Source code
get_significance_stars Man page Source code
ggpicrust2 Man page Source code
gsea_pathway_annotation Man page Source code
gsea_score_label Source code
has_non_default_rownames Source code
import_MicrobiomeAnalyst_daa_results Man page Source code
is_ec_id Source code
is_gene_family_id Source code
is_kegg_pathway_id Source code
is_ko_id Source code
is_ko_level_contrib Source code
is_pathway_id Source code
kegg_abundance Man page
kegg_pathway_reference Man page
ko2kegg_abundance Man page
ko_abundance Man page
ko_reference Man page
ko_to_go_reference Man page
ko_to_kegg_reference Man page
legend_annotation_utils Man page
load_reference_data Source code
log_message Source code
materialize_metadata_sample_column Source code
merge_named_parameters Source code
metacyc_abundance Man page
metacyc_reference Man page
metacyc_to_ec_reference Man page
metadata Man page
negative_log10_probability Source code
normalize_abundance_feature_ids Source code
normalize_annotation_data Source code
normalize_contrib_feature_ids Source code
normalize_contrib_table Source code
normalize_contribution_values Source code
normalize_gsea_scale Source code
normalize_level_colors Source code
normalize_logical_flag Source code
normalize_microbiomeanalyst_column_name Source code
parse_leading_edges Source code
parse_taxonomy_string Source code
pathway_annotation Man page Source code
pathway_daa Man page Source code
pathway_errorbar Man page Source code
pathway_errorbar_table Man page Source code
pathway_gsea Man page Source code
pathway_heatmap Man page Source code
pathway_pca Man page Source code
pathway_ridgeplot Man page Source code
pathway_volcano Man page Source code
perform_aldex2_analysis Source code
perform_deseq2_analysis Source code
perform_edger_analysis Source code
perform_lefser_analysis Source code
perform_limma_voom_analysis Source code
perform_linda_analysis Source code
perform_maaslin2_analysis Source code
perform_metagenomeseq_analysis Source code
permutation_spearman_p_value Source code
prepare_gene_sets Man page Source code
prepare_integer_counts Source code
prepare_maaslin2_feature_mapping Source code
prepare_model_group_column Source code
prepare_spearman_rank_matrix Source code
preview_color_theme Man page Source code
process_kegg_annotations Source code
read_abundance_file Source code
read_contrib_file Man page Source code
read_contribution_input Source code
read_pathway_contrib_file Man page Source code
read_strat_file Man page Source code
require_column Man page Source code
require_package Source code
resolve_annotation_overlaps Man page Source code
resolve_contrib_feature_level Source code
resolve_contribution_annotation_columns Source code
resolve_deprecated_p_adjust_method Source code
resolve_function_id_column Source code
resolve_limma_contrast Man page Source code
resolve_metagenomeseq_css_quantile Source code
resolve_microbiomeanalyst_column Source code
resolve_preranked_comparison Source code
rewrite_kegg_pathway_organism Source code
run_fgsea Man page Source code
run_limma_gsea Man page Source code
run_paired_aldex2_comparison Source code
run_paired_metagenome_daa Source code
run_paired_wilcoxon_comparison Source code
safe_extract Man page Source code
samples_match Source code
smart_color_selection Man page Source code
standardize_microbiomeanalyst_columns Source code
stop_feature_level_conflict Source code
stop_mixed_contrib_feature_levels Source code
summarize_abundance_by_group Source code
summarize_spearman_pair Source code
taxa_contribution_bar Man page Source code
taxa_contribution_heatmap Man page Source code
validate_abundance Source code
validate_and_align_aldex2_effect_results Source code
validate_and_align_backend_result_values Source code
validate_auto_or_positive_number Source code
validate_choice Source code
validate_color_values Source code
validate_compare_gsea_daa_set_direction Source code
validate_complete_design_variables Source code
validate_contrib_feature_level_column Source code
validate_contrib_key_columns Source code
validate_contribution_values Source code
validate_count_parameter Source code
validate_daa_input Source code
validate_daa_results Man page Source code
validate_dataframe Source code
validate_feature_ids Source code
validate_feature_rownames Source code
validate_finite_numeric_values Source code
validate_gene_sets Source code
validate_group Source code
validate_group_sizes Man page Source code
validate_group_vector_for_summary Source code
validate_gsea_group_after_alignment Source code
validate_gsea_group_labels_after_alignment Source code
validate_gsea_visualization_values Source code
validate_hclust_parameters Source code
validate_linda_feature_ids Source code
validate_maaslin2_results Source code
validate_metacyc_gsea_feature_ids Source code
validate_metadata Source code
validate_nonempty_character_column Source code
validate_nonnegative_finite_matrix Source code
validate_numeric_matrix Source code
validate_optional_character_values Source code
validate_p_adjust_method Source code
validate_positive_integer_or_infinity Source code
validate_positive_number Source code
validate_probability_threshold Source code
validate_probability_values Source code
validate_ranked_list Source code
validate_sample_identifiers Source code
validate_significance_inputs Source code
validate_strat_sample_columns Source code
validate_zero_abundance Source code
visualize_gsea Man page Source code
with_retry Source code
ggpicrust2 documentation built on Oct. 7, 2026, 1:07 a.m.

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