mp_cal_pca {MicrobiotaProcess} | R Documentation

## Principal Components Analysis with MPSE or tbl_mpse object

### Description

Principal Components Analysis with MPSE or tbl_mpse object

### Usage

    mp_cal_pca(.data, .abundance, .dim = 3, action = "add", ...)

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

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

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

### Arguments

`.data` | MPSE or tbl_mpse object
`.abundance` | the name of abundance to be calculated.
`.dim` | integer The number of dimensions to be returned, default is 3.
`action` | character "add" joins the pca result to the object, "only" return a non-redundant tibble with the pca result. "get" return 'prcomp' object.
`...` | additional parameters see also 'prcomp'

### Value

update object or tbl according to the action.

### Author(s)

Shuangbin Xu

### Examples

    data(mouse.time.mpse)
    library(ggplot2)
    mpse <- mouse.time.mpse %>%
              mp_decostand(.abundance=Abundance) %>%
              mp_cal_pca(.abundance=hellinger, action="add")
    mpse
    p1 <- mpse %>% mp_plot_ord(.ord=pca, .group=time, ellipse=TRUE)
    p2 <- mpse %>% mp_plot_ord(.ord=pca, .group=time, .color=time, ellipse=TRUE)
    p1 + scale_fill_manual(values=c("#00AED7", "#009E73"))
    p2 + scale_fill_manual(values=c("#00AED7", "#009E73")) +
         scale_color_manual(values=c("#00AED7", "#009E73"))
    ## Not run:
    # action = "only" to extract the non-redundant tibble to visualize
    tbl <- mouse.time.mpse %>%
              mp_decostand(.abundance=Abundance) %>%
              mp_cal_pca(.abundance=hellinger, action="only")
    tbl
    x <- names(tbl)[grepl("PC1 ", names(tbl))] %>% as.symbol()
    y <- names(tbl)[grepl("PC2 ", names(tbl))] %>% as.symbol()
    ggplot(tbl) +
     geom_point(aes(x=!!x, y=!!y, color=time))

    ## End(Not run)

[Package MicrobiotaProcess version 1.4.4 Index]