mp_plot_alpha-methods: Plotting the alpha diversity between samples or groups.

In xiangpin/MicrobitaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Plotting the alpha diversity between samples or groups.

Description

Plotting the alpha diversity between samples or groups.

Usage

mp_plot_alpha(
  .data,
  .group,
  .alpha = c("Observe", "Shannon"),
  test = "wilcox.test",
  comparisons = NULL,
  step_increase = 0.05,
  ...
)

## S4 method for signature 'MPSE'
mp_plot_alpha(
  .data,
  .group,
  .alpha = c("Observe", "Shannon"),
  test = "wilcox.test",
  comparisons = NULL,
  step_increase = 0.05,
  ...
)

## S4 method for signature 'tbl_mpse'
mp_plot_alpha(
  .data,
  .group,
  .alpha = c("Observe", "Shannon"),
  test = "wilcox.test",
  comparisons = NULL,
  step_increase = 0.05,
  ...
)

## S4 method for signature 'grouped_df_mpse'
mp_plot_alpha(
  .data,
  .group,
  .alpha = c("Observe", "Shannon"),
  test = "wilcox.test",
  comparisons = NULL,
  step_increase = 0.05,
  ...
)

Arguments

.data	MPSE or tbl_mpse object
.group	the column name of sample group information
.alpha	the column name of alpha index after run mp_cal_alpha or mp_cal_pd_metric.
test	the name of the statistical test, default is 'wilcox.test'
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 columns of interest, default is NULL, meaning it will be calculated automatically with the names in the .group.
step_increase	numeric vector with the increase in fraction of total height for every additional comparison to minimize overlap, default is 0.05.
...	additional parameters, see also geom_signif

Author(s)

Shuangbin Xu

Examples

## Not run: 
data(mouse.time.mpse)
mpse <- mouse.time.mpse %>%
        mp_rrarefy() %>%
        mp_cal_alpha(.abundance=RareAbundance)
mpse
p <- mpse %>% 
     mp_plot_alpha(.group=time, .alpha=c(Observe, Shannon, Pielou))
p

## End(Not run)

xiangpin/MicrobitaProcess documentation built on Nov. 6, 2024, 1:15 a.m.