Return a boxplot of every alpha metric per group in the samples table of a tidytaco object. If no alpha metrics are present, all available ones are added.

Usage

tacoplot_alphas(
  ta,
  group_by,
  compare_means = FALSE,
  keep_empty_samples = FALSE,
  subsample_metric = NULL,
  ...
)

Arguments

ta

A tidytacos object.

group_by

The name of a variable in the samples table on which to group the samples.

compare_means

Add the result of a statistical test to the plot, comparing the means of the groups. Default is FALSE.

keep_empty_samples

Whether to discard samples not containing any counts or not. By default these are removed.

subsample_metric

if the alpha diversities are precalculated with add_subsampled_alpha(), choose here "mean" or "median" to represent the alpha diversity.

...

Arguments passed on to ggpubr::stat_compare_means

mapping

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

method

a character string indicating which method to be used for comparing means.

paired

a logical indicating whether you want a paired test. Used only in t.test and in wilcox.test.

method.args

a list of additional arguments used for the test method. For example one might use method.args = list(alternative = "greater") for wilcoxon test.

ref.group

a character string specifying the reference group. If specified, for a given grouping variable, each of the group levels will be compared to the reference group (i.e. control group).

ref.group can be also ".all.". In this case, each of the grouping variable levels is compared to all (i.e. basemean).

comparisons

A list of length-2 vectors. The entries in the vector are either the names of 2 values on the x-axis or the 2 integers that correspond to the index of the groups of interest, to be compared.

hide.ns

logical value. If TRUE, hide ns symbol when displaying significance levels.

label.sep

a character string to separate the terms. Default is ", ", to separate the correlation coefficient and the p.value.

label

character string specifying label type. Allowed values include "p.signif" (shows the significance levels), "p.format" (shows the formatted p value).

label.x.npc,label.y.npc

can be numeric or character vector of the same length as the number of groups and/or panels. If too short they will be recycled.

If numeric, value should be between 0 and 1. Coordinates to be used for positioning the label, expressed in "normalized parent coordinates".
If character, allowed values include: i) one of c('right', 'left', 'center', 'centre', 'middle') for x-axis; ii) and one of c( 'bottom', 'top', 'center', 'centre', 'middle') for y-axis.

label.x,label.y

numeric Coordinates (in data units) to be used for absolute positioning of the label. If too short they will be recycled.

vjust

move the text up or down relative to the bracket.

tip.length

numeric vector with the fraction of total height that the bar goes down to indicate the precise column. Default is 0.03. Can be of same length as the number of comparisons to adjust specifically the tip lenth of each comparison. For example tip.length = c(0.01, 0.03).

If too short they will be recycled.

bracket.size

Width of the lines of the bracket.

step.increase

numeric vector with the increase in fraction of total height for every additional comparison to minimize overlap.

symnum.args

a list of arguments to pass to the function symnum for symbolic number coding of p-values. For example, symnum.args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, Inf), symbols = c("****", "***", "**", "*", "ns")).

In other words, we use the following convention for symbols indicating statistical significance:

ns: p > 0.05
*: p <= 0.05
**: p <= 0.01
***: p <= 0.001
****: p <= 0.0001

geom

The geometric object to use to display the data, either as a ggproto Geom subclass or as a string naming the geom stripped of the geom_ prefix (e.g. "point" rather than "geom_point")

position

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

na.rm

If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().