mp_cal_upset-methods: Calculating the samples or groups for each OTU, the result...

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Calculating the samples or groups for each OTU, the result can be visualized by 'ggupset'

Description

Calculating the samples or groups for each OTU, the result can be visualized by 'ggupset'

Usage

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

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

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

## S4 method for signature 'grouped_df_mpse'
mp_cal_upset(
  .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. which is a treedata object.
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_upset()]

Examples

data(mouse.time.mpse)
mpse <- mouse.time.mpse %>%
        mp_rrarefy() %>%
        mp_cal_upset(.abundance=RareAbundance, .group=time, action="add")
mpse
library(ggplot2)
library(ggupset)
p <- mpse %>% mp_plot_upset(.group=time, .upset=ggupsetOftime)
p
# or set action="only"
## Not run: 
tbl <- mouse.time.mpse %>% 
       mp_rrarefy() %>% 
       mp_cal_upset(.abundance=RareAbundance, .group=time, action="only") 
tbl
p2 <- tbl %>%
      ggplot(aes(x=ggupsetOftime)) +
      geom_bar() +
      ggupset::scale_x_upset() +
      ggupset::theme_combmatrix(combmatrix.label.extra_spacing=30)

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.