Man pages for ggpicrust2
Make 'PICRUSt2' Output Analysis and Visualization Easier
| aggregate_taxa_contributions | Aggregate taxa contributions for visualization |
| build_design_matrix | Build design matrix for limma analysis |
| calculate_abundance_stats | Helper function to calculate abundance statistics for... |
| calculate_log2_fold_change | Calculate log2 fold change with consistent pseudocount... |
| calculate_pseudocount | Calculate data-driven pseudocount for log transformation |
| calculate_rank_metric | Calculate rank metric for GSEA |
| calculate_smart_text_size | Smart Text Size Calculator |
| color_themes | Color Theme System for ggpicrust2 |
| compare_daa_results | Compare the Consistency of Statistically Significant Features |
| compare_gsea_daa | Compare GSEA and DAA results |
| compare_metagenome_results | Compare Metagenome Results |
| create_dendrogram | Create dendrogram plot from hierarchical clustering |
| create_empty_plot | Create empty plot for edge cases |
| create_gradient_colors | Create Gradient Colors |
| create_heatmap_plot | Create heatmap visualization of GSEA results |
| create_legend_theme | Create Enhanced Legend Theme |
| create_network_plot | Create network visualization of GSEA results |
| create_pathway_class_theme | Create Pathway Class Annotation Theme |
| daa_annotated_results_df | Differentially Abundant Analysis Results with Annotation |
| daa_results_df | DAA Results Dataset |
| data_utils | Data Utilities for ggpicrust2 |
| dot-as_color_vector | Internal: coerce user 'scale' input to a vector of colors (or... |
| dot-build_continuous_scale | Internal: build a continuous ggplot2 scale layer from colors... |
| dot-build_discrete_fill_for_direction | Internal: build a discrete fill scale for barplot direction |
| dot-build_heatmap_col_fun | Internal: build a circlize colorRamp2 function for... |
| dot-is_ggplot_scale | Internal: detect if an object is a ggplot2 Scale |
| ec_reference | EC Number Reference Dataset |
| format_pvalue_smart | Smart P-value Formatting |
| generate_nested_colors | Generate colors for nested grouping variables |
| get_available_themes | Get Available Color Themes |
| get_color_theme | Get Color Theme |
| get_significance_colors | Get Significance Colors |
| get_significance_stars | Get Significance Stars |
| ggpicrust2 | This function integrates pathway name/description... |
| gsea_pathway_annotation | Annotate GSEA results with pathway information |
| import_MicrobiomeAnalyst_daa_results | Import Differential Abundance Analysis (DAA) results from... |
| kegg_abundance | KEGG Abundance Dataset |
| kegg_pathway_reference | KEGG Pathway Name Reference Dataset |
| ko2kegg_abundance | Convert KO abundance in picrust2 export files to KEGG pathway... |
| ko_abundance | KO Abundance Dataset |
| ko_reference | KEGG Orthology (KO) Reference Dataset |
| ko_to_go_reference | KO to GO Reference Mapping Dataset |
| ko_to_kegg_reference | KO to KEGG Pathway Reference Data |
| legend_annotation_utils | Legend and Annotation Utilities for ggpicrust2 |
| metacyc_abundance | MetaCyc Abundance Dataset |
| metacyc_reference | MetaCyc Pathway Reference Dataset |
| metacyc_to_ec_reference | MetaCyc Pathway to EC Number Mapping Dataset |
| metadata | Metadata for ggpicrust2 Demonstration |
| pathway_annotation | Pathway information annotation |
| pathway_daa | Differential Abundance Analysis for Predicted Functional... |
| pathway_errorbar | The function pathway_errorbar() is used to visualize the... |
| pathway_errorbar_table | Generate Abundance Statistics Table for Pathway Analysis |
| pathway_gsea | Gene Set Enrichment Analysis for PICRUSt2 output |
| pathway_heatmap | Create pathway heatmap with support for multiple grouping... |
| pathway_pca | Perform Principal Component Analysis (PCA) on functional... |
| pathway_ridgeplot | Ridge Plot for GSEA Results |
| pathway_volcano | Volcano Plot for Pathway Differential Abundance Analysis |
| prepare_gene_sets | Prepare gene sets for GSEA |
| preview_color_theme | Preview Color Theme |
| read_contrib_file | Read PICRUSt2 contribution file |
| read_strat_file | Read PICRUSt2 stratified abundance file |
| require_column | Require a column exists in a data frame |
| resolve_annotation_overlaps | Detect and Resolve Annotation Overlaps |
| run_fgsea | Run fgsea using the recommended fgseaMultilevel method |
| run_limma_gsea | Run limma-based gene set analysis (camera/fry) |
| safe_extract | Safely Extract Elements from a List |
| smart_color_selection | Smart Color Selection |
| taxa_contribution_bar | Stacked bar plot of taxa contributions |
| taxa_contribution_heatmap | Heatmap of taxa contributions across functions |
| validate_daa_results | Validate DAA results data frame |
| validate_group_sizes | Validate group sizes for statistical analysis |
| visualize_gsea | Visualize GSEA results |
