mp_cal_cca-methods: [Partial] [Constrained] Correspondence Analysis with MPSE or...

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

[Partial] [Constrained] Correspondence Analysis with MPSE or tbl_mpse object

Description

[Partial] [Constrained] Correspondence Analysis with MPSE or tbl_mpse object

Usage

mp_cal_cca(.data, .abundance, .formula = NULL, .dim = 3, action = "add", ...)

## S4 method for signature 'MPSE'
mp_cal_cca(.data, .abundance, .formula = NULL, .dim = 3, action = "add", ...)

## S4 method for signature 'tbl_mpse'
mp_cal_cca(.data, .abundance, .formula = NULL, .dim = 3, action = "add", ...)

## S4 method for signature 'grouped_df_mpse'
mp_cal_cca(.data, .abundance, .formula = NULL, .dim = 3, action = "add", ...)

Arguments

.data	MPSE or tbl_mpse object
.abundance	the name of abundance to be calculated.
.formula	Model formula right hand side gives the constraining variables, and conditioning variables can be given within a special function 'Condition' and keep left empty, such as ~ A + B or ~ A + Condition(B), default is NULL.
.dim	integer The number of dimensions to be returned, default is 3.
action	character "add" joins the cca result to the object, "only" return a non-redundant tibble with the cca result. "get" return 'cca' object can be analyzed using the related vegan funtion.
...	additional parameters see also 'cca' of vegan.

Value

update object according action argument

Author(s)

Shuangbin Xu

Examples

library(vegan)
data(varespec, varechem)
mpse <- MPSE(assays=list(Abundance=t(varespec)), colData=varechem)
mpse
mpse %<>% 
    mp_cal_cca(.abundance=Abundance, 
               .formula=~Al + P*(K + Baresoil), 
               action="add")
mpse
mpse %>% mp_plot_ord(.ord=CCA, .group=Al, .size=K, show.sample=FALSE, bg.colour="black", colour="white")

YuLab-SMU/MicrobiotaProcess documentation built on July 26, 2024, 4:21 a.m.