mp_cal_nmds-methods: Nonmetric Multidimensional Scaling 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

Nonmetric Multidimensional Scaling Analysis with MPSE or tbl_mpse object

Description

Nonmetric Multidimensional Scaling Analysis with MPSE or tbl_mpse object

Usage

mp_cal_nmds(
  .data,
  .abundance,
  distmethod = "bray",
  .dim = 2,
  action = "add",
  seed = 123,
  ...
)

## S4 method for signature 'MPSE'
mp_cal_nmds(
  .data,
  .abundance,
  distmethod = "bray",
  .dim = 2,
  action = "add",
  seed = 123,
  ...
)

## S4 method for signature 'tbl_mpse'
mp_cal_nmds(
  .data,
  .abundance,
  distmethod = "bray",
  .dim = 2,
  action = "add",
  seed = 123,
  ...
)

## S4 method for signature 'grouped_df_mpse'
mp_cal_nmds(
  .data,
  .abundance,
  distmethod = "bray",
  .dim = 2,
  action = "add",
  seed = 123,
  ...
)

Arguments

.data	MPSE or tbl_mpse object
.abundance	the name of abundance to be calculated.
distmethod	character the method to calculate distance.
.dim	integer The number of dimensions to be returned, default is 2.
action	character "add" joins the NMDS result to the object, "only" return a non-redundant tibble with the NMDS result. "get" return 'metaMDS' object can be analyzed with related 'vegan' function.
seed	a random seed to make this analysis reproducible, default is 123.
...	additional parameters see also 'mp_cal_dist'.

Value

update object or tbl according to the action.

Author(s)

Shuangbin Xu

Examples

data(mouse.time.mpse)
mpse <- mouse.time.mpse %>%
        mp_decostand(.abundance=Abundance) %>%
        mp_cal_nmds(.abundance=hellinger, distmethod="bray", action="add")
library(ggplot2)
p <- mpse %>% mp_plot_ord(.ord=nmds, 
                          .group=time, 
                          .color=time, 
                          .alpha=0.8, 
                          ellipse=TRUE, 
                          show.sample=TRUE)
p <- p +
     scale_fill_manual(values=c("#00AED7", "#009E73")) + 
     scale_color_manual(values=c("#00AED7", "#009E73"))
## Not run: 
mouse.time.mpse %>%
  mp_decostand(.abundance=Abundance) %>%
  mp_cal_nmds(.abundance=hellinger, distmethod="bray", .dim=2, action="only") -> tbl
tbl
x <- names(tbl)[grepl("NMDS1", names(tbl))] %>% as.symbol()
y <- names(tbl)[grepl("NMDS2", names(tbl))] %>% as.symbol()
library(ggplot2)
tbl %>%
 ggplot(aes(x=!!x, y=!!y, color=time)) +
 geom_point() +
 geom_vline(xintercept=0, color="grey20", linetype=2) +
 geom_hline(yintercept=0, color="grey20", linetype=2) +
 theme_bw() +
 theme(panel.grid=element_blank())

## End(Not run)

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