microViz-package | microViz: microbiome data analysis and visualization |
add_paths | Add paths connecting points on a ggplot scatterplot |
adjacent_side | Simple heatmap helper to get a default adjacent side for another annotation |
anno_abund | DEPRECATED Heatmap annotations helpers |
anno_cat | Create colored rectangle annotations for categorical data |
anno_cat_legend | Convenience function for generating a legend for anno_cat annotations. |
anno_prev | DEPRECATED Heatmap annotations helpers |
anno_sample | Helper to specify simple comp_heatmap annotation for other sample data |
anno_sample_cat | Helper to specify comp_heatmap annotation for categorical sample data |
anno_tax_box | Helper to specify heatmap annotation for showing taxa abundance on boxplot |
anno_tax_density | Helper to specify heatmap annotation for showing taxa abundance density plot |
anno_tax_prev | Helper to specify heatmap annotation for showing taxa prevalence as barplot |
anno_var_box | Helper to specify heatmap annotation for variable distribution boxplots |
anno_var_density | Helper to specify heatmap annotation for variable distribution density plot |
anno_var_hist | Helper to specify heatmap annotation for variable distribution histograms |
bdisp_get | Extract elements from psExtra class |
comp_barplot | Plot (grouped and ordered) compositional barplots |
comp_heatmap | Draw heatmap of microbiome composition across samples |
constraint_lab_style | Create list for ord_plot() *_lab_style arguments |
cor_heatmap | Microbe-to-sample-data correlation heatmap |
cor_test | Simple wrapper around cor.test for y ~ x style formula input |
deprecated-heatmap-annotations | DEPRECATED Heatmap annotations helpers |
distinct_palette | Colour palettes suitable for 20+ categories |
dist_bdisp | Wrapper for vegan::betadisper() |
dist_calc | Calculate distances between pairs of samples in phyloseq object |
dist_calc_seq | Calculate distances between sequential samples in ps_extra/phyloseq object |
dist_get | Extract elements from psExtra class |
dist_permanova | Calculate PERMANOVA after dist_calc() |
heat_grid | set options for drawing gridlines on heatmaps |
heat_numbers | Aesthetic settings for drawing numbers on heatmap tiles |
heat_palette | Easy palettes for ComplexHeatmap |
ibd | IBD study data in phyloseq object. |
info_get | Extract elements from psExtra class |
microViz | microViz: microbiome data analysis and visualization |
old_anno_var_box | DEPRECATED Heatmap annotations helpers |
old_anno_var_hist | DEPRECATED Heatmap annotations helpers |
Ordination-arrows | Create ordination plot vector styling lists |
Ordination-labels | Create list for ord_plot() *_lab_style arguments |
ord_calc | Ordinate samples (arrange by similarity in multiple dimensions) |
ord_explore | Interactively explore microbial compositions of ordinated samples |
ord_get | Extract elements from psExtra class |
ord_order_samples | Sort phyloseq samples by ordination axes scores |
ord_order_taxa | Order taxa in phyloseq by their loading vectors |
ord_plot | Customisable ggplot2 ordination plot |
ord_plot_iris | Circular compositional barplot sorted by ordination angle |
otu_get | Extract elements from psExtra class |
perm_get | Extract elements from psExtra class |
phyloseq_validate | Check for (and fix) common problems with phyloseq objects |
prev | Calculate prevalence from numeric vector |
print.psExtraInfo | Print method for psExtraInfo object |
psExtra-accessors | Extract elements from psExtra class |
psExtra-class | Define psExtra class S4 object |
ps_arrange | Arrange samples in phyloseq by sample_data variables or taxon abundance |
ps_calc_diversity | Calculate diversity index and add to phyloseq sample data |
ps_calc_dominant | Calculate dominant taxon in each phyloseq sample |
ps_calc_richness | Calculate richness estimate and add to phyloseq sample data |
ps_dedupe | De-duplicate phyloseq samples |
ps_drop_incomplete | Deselect phyloseq samples with sample_data missings |
ps_filter | Filter phyloseq samples by sample_data variables |
ps_get | Extract elements from psExtra class |
ps_join | Join a dataframe to phyloseq sample data |
ps_melt | Melt phyloseq data object into large data.frame (tibble) |
ps_mutate | Modify or compute new sample_data in phyloseq object |
ps_otu2samdat | Copy phyloseq otu_table data to sample_data |
ps_reorder | Set order of samples in phyloseq object |
ps_select | Select phyloseq sample_data using dplyr::select syntax |
ps_seriate | Arrange samples in a phyloseq by microbiome similarity |
ps_sort_ord | Sort phyloseq samples by ordination axes scores |
samdat_tbl | Extract elements from psExtra class |
sampleAnnotation | Helper to specify a HeatmapAnnotation for samples in comp_heatmap |
scale_shape_girafe_filled | Filled shapes for ggiraph interactive plots |
shao19 | Gut microbiota relative abundance data from Shao et al. 2019 |
stat_chull | Draw convex hull for a set of points on a ggplot |
taxAnnotation | Helper to specify a HeatmapAnnotation for taxa |
taxatree_edges | Create node and edge dataframes for taxatree_plots |
taxatree_funs | Create node and edge dataframes for taxatree_plots |
taxatree_label | Add logical label column to taxatree_stats dataframe |
taxatree_models | Statistical modelling for individual taxa across multiple ranks |
taxatree_models2stats | Extract statistics from taxatree_models or tax_model output |
taxatree_models_get | Extract elements from psExtra class |
taxatree_nodes | Create node and edge dataframes for taxatree_plots |
taxatree_plotkey | Draw labelled key to accompany taxatree_plots |
taxatree_plots | Plot statistical model results for all taxa on a taxonomic tree |
taxatree_plot_labels | Add labels to taxatree plots/key |
taxatree_stats_get | Extract elements from psExtra class |
taxatree_stats_p_adjust | Adjust p values in taxatree_stats dataframe |
tax_agg | Aggregate taxa and track aggregation in psExtra |
tax_anno | DEPRECATED Heatmap annotations helpers |
tax_filter | Filter rare and/or low abundance taxa from a phyloseq object |
tax_fix | Replace unknown, NA, or short tax_table values |
tax_fix_interactive | Shiny app to help you use tax_fix |
tax_lab_style | Create list for ord_plot() *_lab_style arguments |
tax_model | Statistical modelling for individual taxa in a phyloseq |
tax_models2stats | Extract statistics from taxatree_models or tax_model output |
tax_models_get | Extract elements from psExtra class |
tax_mutate | Modify or compute new taxonomic ranks in phyloseq |
tax_name | Simple way to set unique taxa_names for phyloseq object |
tax_names2rank | Add taxa_names as last column in phyloseq tax_table |
tax_palette | Make a fixed taxa colour palette e.g. for comp_barplot |
tax_palette_plot | tax_palette plotting helper function |
tax_prepend_ranks | Add rank prefixes to phyloseq tax_table values |
tax_rename | Make new phyloseq taxa names from classification and taxon abundance info |
tax_reorder | Reorder taxa in phyloseq object using vector of names |
tax_scale | Mean-center and SD-scale taxa in phyloseq |
tax_select | Subset phyloseq object by (partial) taxa names |
tax_sort | Sort taxa in phyloseq otu_table and tax_table |
tax_sort_ord | Order taxa in phyloseq by their loading vectors |
tax_stats_get | Extract elements from psExtra class |
tax_top | Get names of "top" n taxa |
tax_transform | Transform taxa in phyloseq object and record transformation |
tt_get | Extract elements from psExtra class |
upgrade_ps_extra_to_psExtra | Convert old format "ps_extra" objects to new "psExtra" objects |
varAnnotation | Helper to specify a HeatmapAnnotation for variables in cor_heatmap |
var_anno | DEPRECATED Heatmap annotations helpers |
vec_constraint | Create ordination plot vector styling lists |
vec_tax_all | Create ordination plot vector styling lists |
vec_tax_sel | Create ordination plot vector styling lists |