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

mp_cal_upsetR Documentation

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)

xiangpin/MicrobiotaProcess documentation built on July 24, 2024, 11:44 p.m.