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,
      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(s)

Laurent Gatto

### Examples

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

[Package pRoloc version 1.28.0 Index]