itrax_ordination {itraxR}

Principle Component Analysis on Itrax scan data

Description

Performs and visualises principle component analysis data from Itrax result data

Usage

itrax_ordination(
  dataframe,
  elementsonly = TRUE,
  zeros = "addone",
  transform = TRUE,
  return = "list",
  plot = FALSE
)

Arguments

dataframe

pass the name of a dataframe parsed using "itrax_import()" or "itrax_join()"

elementsonly

if TRUE, only chemical elements are included. If FALSE, the data is passed unfiltered, otherwise a character vector of desired variable names can be supplied

zeros

if "addone", adds one to all values. If "limit", replaces zero values with 0.001. Otherwise a function can be supplied to remove zero values.

transform

binary operator that if TRUE will center-log-transform the data, if FALSE will leave the data untransformed. Otherwise, a function can be supplied to transform the data.

return

if "pca" the output of prcomp() is returned, otherwise "list" is a list including the transformed data, sample scores, and the output of prcomp().

plot

set to true if a biplot is required as a side-effect

Value

either an output of prcomp(), or a list including the input data

Examples

itrax_ordination(CD166_19_S1$xrf, plot = TRUE)