Components based on clustered intensity profiles.

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

plotHeatMap(obj, ...)

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

# S4 method for 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.

Value

plotHeatMap returns the same as heatmap.2 or

heatmaply.

Details

Objects from this class are generated by generateComponentsIntClust

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.

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.

S4 class hierarchy

componentsClust
- componentsIntClust