mp_cal_venn {MicrobiotaProcess} | R Documentation

## Calculating the OTU for each sample or group, the result can be visualized by 'ggVennDiagram'

### Description

Calculating the OTU for each sample or group, the result can be visualized by 'ggVennDiagram'

### Usage

    mp_cal_venn(
      .data,
      .group,
      .abundance = NULL,
      action = "add",
      force = FALSE,
      ...
    )

    ## S4 method for signature 'MPSE'
    mp_cal_venn(
      .data,
      .group,
      .abundance = NULL,
      action = "add",
      force = FALSE,
      ...
    )

    ## S4 method for signature 'tbl_mpse'
    mp_cal_venn(
      .data,
      .group,
      .abundance = NULL,
      action = "add",
      force = FALSE,
      ...
    )

    ## S4 method for signature 'grouped_df_mpse'
    mp_cal_venn(
      .data,
      .group,
      .abundance = NULL,
      action = "add",
      force = FALSE,
      ...
    )

### Arguments

`.data` | MPSE or tbl_mpse object
`.group` | the name of group to be calculated. if it is no provided, the sample will be used.
`.abundance` | the name of otu abundance to be calculated. if it is null, the rarefied abundance will be used.
`action` | character, "add" joins the new information to the tibble of tbl_mpse or rowData of MPSE. "only" and "get" return a non-redundant tibble with the just new information.
`force` | logical whether calculate the relative abundance forcibly when the abundance is not be rarefied, default is FALSE.
`...` | additional parameters.

### Value

update object or tibble according the 'action'

### Author(s)

Shuangbin Xu

### See Also

[mp_plot_venn()]

### Examples

    data(mouse.time.mpse)
    mouse.time.mpse %>%
    mp_rrarefy() %>%
    mp_cal_venn(.abundance=RareAbundance, .group=time, action="add") -> mpse
    mpse
    p <- mpse %>% mp_plot_venn(.venn = vennOftime, .group = time)
    ## Not run:
    # visualized by manual
    library(ggplot2)
    mpse %>%
      mp_extract_sample() %>%
      select(time, vennOftime) %>%
      distinct() %>%
      pull(var=vennOftime, name=time) %>%
      ggVennDiagram::ggVennDiagram()

    ## End(Not run)

[Package MicrobiotaProcess version 1.4.4 Index]