plotMarkers: Plot the values for multivariate markers in block analyses

In mixOmicsTeam/mixOmics: Omics Data Integration Project

Plot the values for multivariate markers in block analyses

Description

Plots the standardised values (after centring and/or scaling) for the selected variables for a given block on a given component. Only applies to block.splsda or block.spls.

Usage

plotMarkers(
  object,
  block,
  markers = NULL,
  comp = 1,
  group = NULL,
  col.per.group = NULL,
  global = FALSE,
  title = NULL,
  violin = TRUE,
  boxplot.width = NULL,
  violin.width = 0.9
)

Arguments

object	An object of class block.splsda or block.spls
block	Name or index of the block to use
markers	Character or integer, only include these markers. If integer, the top 'markers' features are shown
comp	Integer, the component to use
group	Factor, the grouping variable (only required for block.spls objects)
col.per.group	character (or symbol) color to be used when 'group' is defined. Vector of the same length as the number of groups.
global	Logical indicating whether to show the global plots (TRUE) or segregate by feature (FALSE). Only available when object$scale=TRUE
title	The plot title
violin	(if global = FALSE) Logical indicating whether violin plots should also be shown
boxplot.width	Numeric, adjusts the width of the box plots
violin.width	Numeric, adjusts the width of the violin plots

Value

A ggplot object

See Also

plotLoadings, block.splsda, block.spls

Examples

# see ?block.splsda and ?block.spls

mixOmicsTeam/mixOmics documentation built on Oct. 26, 2023, 6:48 a.m.