plot_covariates {autonomics}R Documentation

Biplot covariates

Description

Biplot covariates

Usage

plot_covariates(...)

biplot_covariates(
  object,
  method = "pca",
  covariates = "subgroup",
  ndim = 6,
  dimcols = 1,
  varcols = length(covariates),
  plot = TRUE
)

Arguments

...

used to maintain deprecated functions

object

SummarizedExperiment

method

'pca', 'pls', 'lda', or 'sma'

covariates

covariates: mapped to color or batch-corrected

ndim

number of dimensions to plot

dimcols

number of dimension columns

varcols

number of covariate columns

plot

TRUE or FALSE: whether to plot

Value

ggplot object

See Also

biplot_corrections

Examples

file <- download_data('atkin18.metabolon.xlsx')
object <- read_metabolon(file, pca = TRUE, plot = FALSE)
biplot_covariates(object, covariates = 'Group', ndim = 12, dimcols = 3)
biplot_covariates(object, covariates = c('SEX', 'T2D', 'SUB', 'SET'))
biplot_covariates(object, covariates = c('SEX', 'T2D', 'SUB', 'SET'), ndim=2)
biplot_covariates(object, covariates = c('Group'), dimcols = 3)

[Package autonomics version 1.2.0 Index]