Make 'PICRUSt2' Output Analysis and Visualization Easier
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Documentation for package ‘ggpicrust2’ version 2.5.2
Help Pages
| 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_gradient_colors | Create Gradient Colors |
| create_legend_theme | Create Enhanced Legend Theme |
| 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 |
| format_pvalue_smart | Smart P-value Formatting |
| 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 annotations, ten of the most advanced differential abundance (DA) methods, and visualization of DA results. |
| ggpicrust2_extended | Integrated analysis with ggpicrust2 including GSEA |
| gsea_pathway_annotation | Annotate GSEA results with pathway information |
| import_MicrobiomeAnalyst_daa_results | Import Differential Abundance Analysis (DAA) results from MicrobiomeAnalyst |
| kegg_abundance | KEGG Abundance Dataset |
| ko2kegg_abundance | Convert KO abundance in picrust2 export files to KEGG pathway abundance |
| ko_abundance | KO Abundance Dataset |
| legend_annotation_utils | Legend and Annotation Utilities for ggpicrust2 |
| metacyc_abundance | MetaCyc Abundance Dataset |
| metadata | Metadata for ggpicrust2 Demonstration |
| pathway_annotation | Pathway information annotation |
| pathway_errorbar | The function pathway_errorbar() is used to visualize the results of functional pathway differential abundance analysis as error bar plots. |
| 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 variables |
| pathway_pca | Perform Principal Component Analysis (PCA) on functional pathway abundance data |
| prepare_gene_sets | Prepare gene sets for GSEA |
| preview_color_theme | Preview Color Theme |
| resolve_annotation_overlaps | Detect and Resolve Annotation Overlaps |
| safe_extract | Safely Extract Elements from a List |
| smart_color_selection | Smart Color Selection |
| visualize_gsea | Visualize GSEA results |