Generates boxplots of the most abundant taxa.
amp_boxplot( data, group_by = "Sample", sort_by = "median", plot_type = "boxplot", point_size = 1, tax_aggregate = "Genus", tax_add = NULL, tax_show = 20, tax_empty = "best", tax_class = NULL, order_group = NULL, order_y = NULL, plot_flip = FALSE, plot_log = FALSE, adjust_zero = NULL, normalise = TRUE, detailed_output = FALSE )
(required) Data list as loaded with
Group the samples by a variable in the metadata.
Sort the boxplots by
The size of points. (default:
The taxonomic level to aggregate the OTUs. (default:
Additional taxonomic level(s) to display, e.g.
The number of taxa to show, or a vector of taxa names. (default:
How to show OTUs without taxonomic information. One of the following:
Converts a specific phylum to class level instead, e.g.
A vector to order the groups by.
A vector to order the y-axis by.
(logical) Flip the axes of the plot axis. (default:
(logical) Log10-scale the plot. (default:
Keep abundances of 0 in the calculation of medians by adding this value. (default:
(logical) Transform the OTU read counts to be in percent per sample. (default:
(logical) Return additional details or not. If
A ggplot2 object. If
detailed_output = TRUE a list with a ggplot2 object and additional data.
# Load example data data("AalborgWWTPs") # 10 boxplots grouped by WWTP with phylum name added amp_boxplot(AalborgWWTPs, group_by = "Plant", tax_show = 10, tax_add = "Phylum" )