plot_taxa_composition.Rd
Plot taxon abundance for samples. It is a legacy function from microbiome
.
plot_taxa_composition(x, sample.sort = NULL, taxonomic.level = "Phylum", transform = "compositional", otu.sort = NULL, palette = brewer.pal(12, "Paired"), x.label = "sample", plot.type = "barplot", average_by = NULL, verbose = FALSE, mar = c(5, 12, 1, 1), ...)
x |
|
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sample.sort | Order samples. Various criteria are available:
|
taxonomic.level | Merge the OTUs (for phyloseq object) into a higher taxonomic level. This has to be one from colnames(tax_table(x)). |
transform | Data transform to be used in plotting (but not in sample/taxon ordering). The options are 'Z-OTU', 'Z-Sample', 'log10' and 'compositional'. See the |
otu.sort | Order taxa. Same options as for the sample.sort argument but instead of metadata, taxonomic table is used. Also possible to sort by 'abundance'. |
palette | The number and palette |
x.label | Specify how to label the x axis. This should be one of the variables in sample_variables(x). |
plot.type | Plot type: 'barplot' or 'lineplot'. |
average_by | Variable to group. |
verbose | verbose. |
mar | Figure margins. |
... | Arguments to be passed (for |
A ggplot
plot object.
# NOT RUN { # Example data library(microbiome) library(microbiomeutilities) data("biogeogut") pseq <- biogeogut plot_taxa_composition(pseq, taxonomic.level = "Phylum") # }