LorMe (version 1.2.1)

Alpha_diversity_calculator2: 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
)

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

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).

Author

Wang Ningqi

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)