mp_cal_pcoa {MicrobiotaProcess} | R Documentation

## Principal Coordinate Analysis with MPSE or tbl_mpse object

### Description

Principal Coordinate Analysis with MPSE or tbl_mpse object

### Usage

    mp_cal_pcoa(
      .data,
      .abundance,
      distmethod = "bray",
      .dim = 3,
      action = "add",
      ...
    )

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

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

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

### 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 3.
`action` | character "add" joins the pca result to the object and the 'pcoa' object also was add to the internal attributes of the object, "only" return a non-redundant tibble with the pca result. "get" return 'pcoa' object.
`...` | 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)
    mpse
    mpse %<>% mp_cal_pcoa(.abundance=hellinger, stmethod="bray", action="add")
    library(ggplot2)
    p <- mpse %>% mp_plot_ord(.ord=pcoa, .group=time, .color=time, ellipse=TRUE)
    p <- p +
         scale_fill_manual(values=c("#00AED7", "#009E73")) +
         scale_color_manual(values=c("#00AED7", "#009E73"))
    ## Not run:
    # Or run with action='only' and return tbl_df to visualize manual.
    mouse.time.mpse %>%
      mp_decostand(.abundance=Abundance) %>%
      mp_cal_pcoa(.abundance=hellinger, distmethod="bray", .dim=2, action="only") -> tbl
    tbl
    x <- names(tbl)[grepl("PCo1 ", names(tbl))] %>% as.symbol()
    y <- names(tbl)[grepl("PCo2 ", names(tbl))] %>% as.symbol()
    library(ggplot2)
    tbl %>%
     ggplot(aes(x=!!x, y=!!y, color=time)) +
     stat_ellipse(aes(fill=time), geom="polygon", alpha=0.5) +
     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)

[Package MicrobiotaProcess version 1.4.4 Index]