Alpha_diversity_calculator2: Calculate alpha diversity based on tax summary object or...

In LorMe: Lightening One-Code Resolving Microbial Ecology Solution

Calculate alpha diversity based on tax summary object or dataframe table

Description

Calculate alpha diversity of each sample

Usage

Alpha_diversity_calculator2(
  taxobj = NULL,
  taxlevel = NULL,
  prefix = "",
  input,
  inputformat,
  reads
)

Arguments

taxobj	tax summary objects computed by tax_summary. Default:NULL.
taxlevel	taxonomy levels used for visualization.Must be one of c("Domain","Phylum","Class","Order","Family","Genus","Species","Base").Default:NULL.
prefix	A character string as prefix of diversity index. Default:""
input	Reads or relative abundance of OTU/Taxa/gene data frame,see details in inputformat. (Useless when taxobj is set).
inputformat	(Useless when taxobj is set) 1:data frame with first column of OTUID and last column of taxonomy 2:data frame with first column of OTUID/taxonomy 3:data frame of all numeric
reads	If the input data frame were from reads table or not(relative abundance table).(Useless when taxobj is set).

Value

when tax taxobj is set, returns column table with group information combined with for alpha-diversity of each sample,else returns data frame for alpha-diversity of each sample

Note

1.When input data frame is in relative abundance table,Chao and ACE are not available

Author(s)

Wang Ningqi [e-mail]

Examples

### Data preparation ####
data(testotu)
groupinformation <- data.frame(
  group = c(rep("a", 10), rep("b", 10)),
  factor1 = rnorm(10),
  factor2 = rnorm(mean = 100, 10),
  subject = factor(c(1:10, 1:10))
)

# Summary OTU table into genus table and phylum table
testtax_summary <- tax_summary(
  groupfile = groupinformation,
  inputtable = testotu[, 2:21],
  reads = TRUE,
  taxonomytable = testotu[, c(1, 22)]
)

### Use taxsummary object as input ###
Alpha <- Alpha_diversity_calculator2(
  taxobj = testtax_summary,
  taxlevel = "Base"
)
head(Alpha)

# In genus level
Alpha <- Alpha_diversity_calculator2(
  taxobj = testtax_summary,
  taxlevel = "Genus",
  prefix = "Genus"
)
head(Alpha)

### Input dataframe from reads table ###
Alpha <- Alpha_diversity_calculator2(
  input = testotu,
  prefix = "Bacterial",
  inputformat = 1,
  reads = TRUE
)

### Input dataframe from relative abundance table ###
if (!require(magrittr)) install.packages("magrittr")
library(magrittr)
Alpha <- Filter_function(
  input = testotu,
  threshold = 0,
  format = 1
) %>%
  Alpha_diversity_calculator2(
    input = .,
    prefix = "Bacterial",
    inputformat = 1,
    reads = FALSE
  )
head(Alpha)

LorMe documentation built on Sept. 13, 2024, 9:07 a.m.