R: Draw a dendrogram of subcellular clusters

mrkHClust {pRoloc}

R Documentation

Draw a dendrogram of subcellular clusters

Description

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, 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.
`plot`	A `logical` defining whether the dendrogram should be plotted. Default is `TRUE`.
`...`	Additional parameters passed when plotting the `dendrogram`.

Value

Invisibly returns a matrix of average occupancy profiles for all marker classes defined in fcol.

Author(s)

Laurent Gatto

Examples

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

[Package pRoloc version 1.20.2 Index]