Generates boxplots of the most abundant taxa.
amp_boxplot(
data,
group_by = NULL,
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
)Arguments
- data
(required) Data list as loaded with
amp_load.- group_by
Group the samples by a variable in the metadata.
- sort_by
Generic function name to use for sorting most abundant taxa, fx
mean,median, orsum. (default:median)- plot_type
Plot type.
"boxplot"or"point". (default:"boxplot")- point_size
The size of points. (default:
1)- tax_aggregate
The taxonomic level to aggregate the OTUs. (default:
"Genus")- tax_add
Additional taxonomic level(s) to display, e.g.
"Phylum". (default:"none")- tax_show
The number of taxa to show, or a vector of taxa names. (default:
20)- tax_empty
How to show OTUs without taxonomic information. One of the following:
"remove": Remove OTUs without taxonomic information."best": (default) Use the best classification possible."OTU": Display the OTU name.
- tax_class
Converts a specific phylum to class level instead, e.g.
"p__Proteobacteria".- order_group
A vector to order the groups by.
- order_y
A vector to order the y-axis by.
- plot_flip
(logical) Flip the axes of the plot axis. (default:
FALSE)- plot_log
(logical) Log10-scale the plot. (default:
FALSE)- adjust_zero
Keep abundances of 0 in the calculation of medians by adding this value. (default:
NULL)- normalise
(logical) Transform the OTU read counts to be in percent per sample. (default:
TRUE)
Value
A ggplot2 object. If detailed_output = TRUE a list with a ggplot2 object and additional data.
See also
Examples
# 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"
)
