combine_and_translate: Combine data for visualization

In LorMe: Lightening One-Code Resolving Microbial Ecology Solution

Combine data for visualization

Description

Combine group information and index into data frame for visualization(scatter, bar plot, alluvial,box plot etc.).

Usage

combine_and_translate(inputframe, groupframe, itemname, indexname, inputtype)

Arguments

inputframe	Data frame of index ,sample ID in column,requires all numeric(e.g. result from Alpha_diversity_calculator or Top_taxa function)
groupframe	Data frame of group information(and other abiotic/geographic factors)
itemname	A character string of your inputframe itemname
indexname	A character string of your inputframe indexname
inputtype	If sample ID were in row and index in column in inputframe.

Value

key-value pairs data frame

Author(s)

Wang [e-mail]

Examples

{
  require(magrittr)
  data(testotu)

  ## Data preparation ##
  Alpha <- Alpha_diversity_calculator2(
    input = testotu,
    prefix = "Bacterial",
    inputformat = 1,
    reads = TRUE
  )

  topotu <- data.frame(
    Top_taxa(
      input = testotu,
      n = 10,
      inputformat = 1,
      outformat = 1
    )[, -1],
    row.names = paste0(rep("otu", 11), 1:11)
  )

  groupinformation1 <- data.frame(
    group = c(rep("a", 10), rep("b", 10)),
    factor1 = rnorm(10),
    factor2 = rnorm(mean = 100, 10)
  )

  ### Use inputtype = FALSE ###
  head(Alpha)
  combine_and_translate(
    Alpha, groupinformation1,
    itemname = "Alpha", indexname = "index",
    inputtype = FALSE
  )

  ### Use inputtype = TRUE ###
  head(topotu)
  combine_and_translate(
    topotu, groupinformation1,
    itemname = "OTU", indexname = "reads",
    inputtype = TRUE
  )
}

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