mp_cal_rarecurve-methods: Calculating the different alpha diversities index with...

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

Calculating the different alpha diversities index with different depth

Description

Calculating the different alpha diversities index with different depth

Usage

mp_cal_rarecurve(
  .data,
  .abundance = NULL,
  action = "add",
  chunks = 400,
  seed = 123,
  force = FALSE,
  ...
)

## S4 method for signature 'MPSE'
mp_cal_rarecurve(
  .data,
  .abundance = NULL,
  action = "add",
  chunks = 400,
  seed = 123,
  force = FALSE,
  ...
)

## S4 method for signature 'tbl_mpse'
mp_cal_rarecurve(
  .data,
  .abundance = NULL,
  action = "add",
  chunks = 400,
  seed = 123,
  force = FALSE,
  ...
)

## S4 method for signature 'grouped_df_mpse'
mp_cal_rarecurve(
  .data,
  .abundance = NULL,
  action = "add",
  chunks = 400,
  seed = 123,
  force = FALSE,
  ...
)

Arguments

.data	MPSE or tbl_mpse object
.abundance	the name of otu abundance to be calculated.
action	character it has three options, "add" joins the new information to the input tbl (default), "only" return a non-redundant tibble with the just new information, ang 'get' return a 'rarecurve' object.
chunks	numeric the split number of each sample to calculate alpha diversity, default is 400. eg. A sample has total 40000 reads, if chunks is 400, it will be split to 100 sub-samples (100, 200, 300,..., 40000), then alpha diversity index was calculated based on the sub-samples.
seed	a random seed to make the result reproducible, default is 123.
force	logical whether calculate rarecurve forcibly when the '.abundance' is not be rarefied, default is FALSE
...	additional parameters.

Value

update rarecurce calss

Author(s)

Shuangbin Xu

See Also

[mp_plot_rarecurve()] and [mp_extract_rarecurve()]

Examples

data(mouse.time.mpse)
mouse.time.mpse %>% 
mp_rrarefy() -> mpse
mpse
# larger 'chunks' means more robust, but it will become slower.
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=c("Observe", "ACE"))

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