Draw a dendrogram of subcellular clusters

This functions calculates an average protein profile for each marker class (proteins of unknown localisation are ignored) and then generates a dendrogram representing the relation between marker classes. The colours used for the dendrogram labels are taken from the default colours (see getStockcol) so as to match the colours with other spatial proteomics visualisations such as plot2D.

Usage

mrkHClust(
  object,
  fcol = "markers",
  distargs,
  hclustargs,
  method = mean,
  plot = TRUE,
  ...
)

Arguments

object

An instance of class MSnSet.

fcol

Feature meta-data label (fData column name) defining the groups to be differentiated using different colours. Default is markers.

distargs

A list of arguments to be passed to the dist function.

hclustargs

A list of arguments to be passed to the hclust function.

method

A function to average marker profiles. Default is mean.

plot

A logical defining whether the dendrogram should be plotted. Default is TRUE.

...

Additional parameters passed when plotting the dendrogram.

Value

Invisibly returns a dendrogram object, containing the hierarchical cluster as computed by hclust.

Author

Laurent Gatto

Examples

library("pRolocdata")
data(dunkley2006)
mrkHClust(dunkley2006)