mp_plot_abundance {MicrobiotaProcess} | R Documentation

## plotting the abundance of taxa via specified taxonomy class

### Description

plotting the abundance of taxa via specified taxonomy class

### Usage

    mp_plot_abundance(
      .data,
      .abundance = NULL,
      .group = NULL,
      taxa.class = NULL,
      topn = 10,
      relative = TRUE,
      force = FALSE,
      plot.group = FALSE,
      ...
    )

    ## S4 method for signature 'MPSE'
    mp_plot_abundance(
      .data,
      .abundance = NULL,
      .group = NULL,
      taxa.class = NULL,
      topn = 10,
      relative = TRUE,
      force = FALSE,
      plot.group = FALSE,
      ...
    )

    ## S4 method for signature 'tbl_mpse'
    mp_plot_abundance(
      .data,
      .abundance = NULL,
      .group = NULL,
      taxa.class = NULL,
      topn = 10,
      relative = TRUE,
      force = FALSE,
      plot.group = FALSE,
      ...
    )

    ## S4 method for signature 'grouped_df_mpse'
    mp_plot_abundance(
      .data,
      .abundance = NULL,
      .group = NULL,
      taxa.class = NULL,
      topn = 10,
      relative = TRUE,
      force = FALSE,
      plot.group = FALSE,
      ...
    )

### Arguments

`.data` | MPSE object or tbl_mpse object
`.abundance` | the column name of abundance to be plotted.
`.group` | the column name of group to be calculated and plotted, default is NULL.
`taxa.class` | name of taxonomy class, default is NULL, meaning the Phylum class will be plotted.
`topn` | integer the number of the top most abundant, default is 10.
`relative` | logical whether calculate the relative abundance and plotted.
`force` | logical whether calculate the relative abundance forcibly when the abundance is not be rarefied, default is FALSE.
`plot.group` | logical whether plotting the abundance of specified taxa.class taxonomy with group not sample level, default is FALSE.
`...` | additional parameters, meaningless now.

### Author(s)

Shuangbin Xu

### Examples

    ## Not run:
    data(mouse.time.mpse)
    mouse.time.mpse %<>%
      mp_rrarefy()
    mouse.time.mpse
    mouse.time.mpse %<>%
      mp_cal_abundance(.abundance=RareAbundance, action="add") %>%
      mp_cal_abundance(.abundance=RareAbundance, .group=time, action="add")
    mouse.time.mpse
    p1 <- mouse.time.mpse %>%
          mp_plot_abundance(.abundance=RelRareAbundanceBySample,
                            .group=time,
                            taxa.class="Phylum",
                            topn=20)
    p2 <- mouse.time.mpse %>%
          mp_plot_abundance(.abundance = Abundance,
                            taxa.class = Phylum,
                            topn = 20,
                            relative = FALSE,
                            force = TRUE
                           )
    p3 <- mouse.time.mpse %>%
          mp_plot_abundance(.abundance = RareAbundance,
                            .group = time,
                            taxa.class = Phylum,
                            topn = 20,
                            relative = FALSE,
                            force = TRUE
                            )
    p4 <- mouse.time.mpse %>%
          mp_plot_abundance(.abundance = RareAbundance,
                            .group = time,
                            taxa.class = Phylum,
                            topn = 20,
                            relative = FALSE,
                            force = TRUE,
                            plot.group = TRUE
                            )

    ## End(Not run)

[Package MicrobiotaProcess version 1.4.4 Index]