Man pages for TBrach/MicrobiomeX
eXtended Functions for Microbiome Analysis and Visualization
| biplot_bca | Draw a between class analysis (BCA) plot. |
| biplot_pcoa | Draw a principal coordinate biplot using Bray-Curtis... |
| boxplot_taxon | Make boxplot of taxon abundance stratified by one sample... |
| distance_t_analyse | Within- and between-group beta-diversity analysis |
| draw_taxa_heatmap | Draw a heatmap of the OTU abundances in a phyloseq object. |
| filter_results | Filter differential test results for specific taxa |
| format_hits | Format differential test results to be presentable |
| format_hits_for_heatmap | Format significant hits results so that it can be shown as an... |
| get_my_palette_colors | Get palette color maps for a variable from a custom palette... |
| get_my_palette_name | Get the name of the custom palette for a given variable |
| get_permanova_table | Make knitr table from Permanova results |
| get_pretty_taxon_name | Get presentable name for a taxon |
| get_significance_string | Get statistical significance level strings for P-values. |
| get_taxon_by_id | Get taxonomy annotation for a given id in a phyloseq object |
| gm_own | Calculate geometric mean of a vector. |
| hello | Hello, World! |
| knit_hits_table | Make knitr table of differential results |
| make_heat_map_from_physeq | Internal function to draw heatmap from a physeq object. |
| plot_pcoa | Draw a principal coordinate plot using Bray-Curtis... |
| run_contrast_2_levels | Extract DESeq2 results |
| tabulate_factors | Tabulate interaction between two factors in the sample_data... |
| test_differential_abundance_DESeq2 | DESeq2 - negative binomial Wald test |
| test_differential_abundance_Kruskal | Kruskal-Wallis differential abundance test |
| test_differential_abundance_Wilcoxon | Wilcoxon rank sum differential abundance test |
| test_differential_prevalence | Differential prevalence testing |
