mp_plot_rarecurve {MicrobiotaProcess} | R Documentation

## Rarefaction alpha index with MPSE

### Description

Rarefaction alpha index with MPSE

### Usage

    mp_plot_rarecurve(
      .data,
      .rare,
      .alpha = c("Observe", "Chao1", "ACE"),
      .group = NULL,
      nrow = 1,
      plot.group = FALSE,
      ...
    )

    ## S4 method for signature 'MPSE'
    mp_plot_rarecurve(
      .data,
      .rare,
      .alpha = c("Observe", "Chao1", "ACE"),
      .group = NULL,
      nrow = 1,
      plot.group = FALSE,
      ...
    )

    ## S4 method for signature 'tbl_mpse'
    mp_plot_rarecurve(
      .data,
      .rare,
      .alpha = c("Observe", "Chao1", "ACE"),
      .group = NULL,
      nrow = 1,
      plot.group = FALSE,
      ...
    )

    ## S4 method for signature 'grouped_df_mpse'
    mp_plot_rarecurve(
      .data,
      .rare,
      .alpha = c("Observe", "Chao1", "ACE"),
      .group = NULL,
      nrow = 1,
      plot.group = FALSE,
      ...
    )

### Arguments

`.data` | MPSE object or tbl_mpse after it was performed `mp_cal_rarecurve` with `action='add'`
`.rare` | the column names of
`.alpha` | the names of alpha index, which should be one or more of Observe, ACE, Chao1, default is Observe.
`.group` | the column names of group, default is NULL, when it is provided, the rarecurve lines will group and color with the `group`.
`nrow` | integer Number of rows in `facet_wrap`.
`plot.group` | logical whether to combine the samples, default is FALSE, when it is TRUE, the samples of same group will be represented by their group.
`...` | additional parameters, see also `geom_smooth`.

### Author(s)

Shuangbin Xu

### Examples

    ## Not run:
    data(mouse.time.mpse)
    mpse <- mouse.time.mpse %>%
            mp_rrarefy()
    mpse
    mpse %<>% mp_cal_rarecurve(.abundance=RareAbundance, chunks=100, action="add")
    mpse
    p1 <- mpse %>% mp_plot_rarecurve(.rare=RareAbundanceRarecurve, .alpha="Observe")
    p2 <- mpse %>% mp_plot_rarecurve(.rare=RareAbundanceRarecurve, .alpha="Observe", .group=time)
    p3 <- mpse %>% mp_plot_rarecurve(.rare=RareAbundanceRarecurve, .alpha="Observe", .group=time, plot.group=TRUE)

    ## End(Not run)

[Package MicrobiotaProcess version 1.4.4 Index]