componentsIntClust-class: Components based on clustered intensity profiles.

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Components based on clustered intensity profiles.

Description

This class is derived from componentsClust and is used to store hierarchical clustering information from intensity profiles of feature groups.

Usage

plotHeatMap(obj, ...)

## S4 method for signature 'componentsIntClust'
plotHeatMap(
  obj,
  interactive = FALSE,
  col = NULL,
  margins = c(6, 2),
  cexCol = 1,
  ...
)

## S4 method for signature 'componentsIntClust'
plotInt(
  obj,
  index,
  pch = 20,
  type = "b",
  lty = 3,
  col = NULL,
  plotArgs = NULL,
  linesArgs = NULL
)

Arguments

obj	A componentsIntClust object.
...	Further options passed to heatmap.2 / heatmaply (plotHeatMap).
interactive	If TRUE an interactive heatmap will be drawn (with heatmaply).
col	The colour used for plotting. Set to NULL for automatic colours.
margins, cexCol	Passed to heatmap.2
index	Numeric component/cluster index or component name.
pch, type, lty	Passed to lines.
plotArgs, linesArgs	A list with further arguments passed to plot and lines, respectively.

Details

Objects from this class are generated by generateComponentsIntClust

Value

plotHeatMap returns the same as heatmap.2 or heatmaply.

Methods (by generic)

• plotHeatMap(componentsIntClust): draws a heatmap using the heatmap.2 or heatmaply function.

• plotInt(componentsIntClust): makes a plot for all (normalized) intensity profiles of the feature groups within a given cluster.

Slots

clusterm

Numeric matrix with normalized feature group intensities that was used for clustering.

S4 class hierarchy

• componentsClust

  • componentsIntClust

Note

When the object is altered (e.g. by filtering or subsetting it), methods that need the original clustered data such as plotting methods do not work anymore and stop with an error.

See Also

componentsClust for other relevant methods and generateComponents

rickhelmus/patRoon documentation built on Nov. 22, 2024, 3:11 p.m.