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
.
mrkHClust(
object,
fcol = "markers",
distargs,
hclustargs,
method = mean,
plot = TRUE,
...
)
An instance of class MSnSet
.
Feature meta-data label (fData column name) defining
the groups to be differentiated using different
colours. Default is markers
.
A list
of arguments to be passed to the
dist
function.
A list
of arguments to be passed to the
hclust
function.
A function
to average marker
profiles. Default is mean
.
A logical
defining whether the dendrogram
should be plotted. Default is TRUE
.
Additional parameters passed when plotting the
dendrogram
.
Invisibly returns a dendrogram object, containing the
hierarchical cluster as computed by hclust
.
library("pRolocdata")
data(dunkley2006)
mrkHClust(dunkley2006)