Visualize a sankey diagram from taxonomic lineages from one or many samples
plot_taxonomy_annotate_sankey.Rd`plot_taxonomy_annotate_sankey()` plots a sankey diagram from the output of sourmash taxonomy annotate. The input data frame can contain one or many samples. If there are many samples, abundances of each lineage are summarized and sample-level information is lost. If the parameter `tax_glom_level` is specified, the plot will be summarized to that taxonomic rank (e.g. if "order" is specified, only domain, phylum, class, and order will be plotted).
Usage
plot_taxonomy_annotate_sankey(
taxonomy_annotate_df,
tax_glom_level = NULL,
palette = NULL,
label = TRUE
)Arguments
- taxonomy_annotate_df
Data frame containing outputs from sourmash taxonomy annotate. Can contain results from one or many runs of sourmash taxonomy annotate. If specified, agglomeration occurs across all queries.
- tax_glom_level
Optional character string specifying the taxonomic rank to agglomerate k-mer counts. Must be one of "domain", "phylum", "class", "order", "family", "genus", "species."
- palette
Optional character vector specifying a palette. Colors in the palette are recycled across taxonomic labels. If no palette is specified, RColorBrewer's Set2 is the default.
- label
Boolean controlling whether taxonomy labels are added to the plot. The default, TRUE, plots labels. Setting to FALSE removes the labels and can be used to control the label appearances; add a layer with `ggforce::geom_parallel_sets_labels()` to re-add labels and use arguments passed to `ggplot2::layer()` to control the appearance of the output.