plot_composition {microbiome} | R Documentation |
Plot taxon abundance for samples.
plot_composition(x, sample.sort = NULL, otu.sort = NULL, x.label = "sample", plot.type = "barplot", verbose = FALSE, average_by = NULL, ...)
x |
|
sample.sort |
Order samples. Various criteria are available:
|
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'. |
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 'heatmap' |
verbose |
verbose
(but not in sample/taxon ordering).
The options are 'Z-OTU', 'Z-Sample', 'log10' and 'compositional'.
See the |
average_by |
Average the samples by the average_by variable |
... |
Arguments to be passed (for |
A ggplot
plot object.
library(dplyr) data(atlas1006) pseq <- atlas1006 %>% subset_samples(DNA_extraction_method == "r") %>% aggregate_taxa(level = "Phylum") %>% transform(transform = "compositional") p <- plot_composition(pseq, sample.sort = "Firmicutes", otu.sort = "abundance", verbose = TRUE) + scale_fill_manual(values = default_colors("Phylum")[taxa(pseq)])