object_config: Set taxonomy summary configuration

In LorMe: Lightening One-Code Resolving Microbial Ecology Solution

Set taxonomy summary configuration

Description

This function set taxonomy summary configuration by assigning treatment column number, facet column number, replication column number, treatment mapping color, treatment order and facet order.

Usage

object_config(
  taxobj,
  treat_location,
  facet_location = NULL,
  rep_location,
  subject_location = NULL,
  treat_col = NULL,
  treat_order = NULL,
  facet_order = NULL
)

Arguments

taxobj	Taxonomic summary object generated by tax_summary
treat_location	Numeric. Treatment column number in metafile/groupinformation.
facet_location	Numeric, default:NULL. Facet column number in metafile/groupinformation.
rep_location	Numeric. Replication column number in metafile/groupinformation.
subject_location	Numeric, default:NULL.Subject column number in metafile/groupinformation (used for pairwise experiment).
treat_col	Named character string, default:NULL. A set of aesthetic character to map treatment to.
treat_order	Character string, default:NULL. The character string indicating treatment displaying order.
facet_order	Character string, default:NULL. The character string indicating facet displaying order.

Value

object_config returns taxonomy summary object with configuration.

Author(s)

Wang [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)),
    group2 = c(rep("e", 5), rep("f", 5), rep("e", 5), rep("f", 5))
  )

  ### Packaging metafile, community data, and taxonomy table ###
  test_object <- tax_summary(
    groupfile = groupinformation,
    inputtable = testotu[, 2:21],
    reads = TRUE,
    taxonomytable = testotu[, c(1, 22)]
  )

  ### Object configuration ###
  test_object_plan1 <- object_config(
    taxobj = test_object,
    treat_location = 1,
    rep_location = 4
  )

  ### Facet configuration ###
  test_object_plan2 <- object_config(
    taxobj = test_object,
    treat_location = 1,
    rep_location = 4,
    facet_location = 5
  )
}

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