biplot_covariates: Biplot covariates

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Biplot covariates

Description

Biplot covariates

Usage

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

Arguments

object	SummarizedExperiment
method	'pca', 'pls', 'lda', or 'sma'
by	svar
block	svar
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 <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
object <- read_metabolon(file, pca = TRUE)
biplot_covariates(object, covariates = 'subgroup', ndim = 12, dimcols = 3)
biplot_covariates(object, covariates = c('Sex', 'Diabetes', 'Subject', 'Time'))
biplot_covariates(object, covariates = c('Sex', 'Diabetes', 'Subject', 'Time'), ndim = 2)
biplot_covariates(object, covariates = c('subgroup'), dimcols = 3)

bhagwataditya/autonomics documentation built on Dec. 1, 2024, 12:27 a.m.