get_signatures-HierarchicalPartition-method {cola}R Documentation

Get signatures rows

Description

Get signatures rows

Usage

## S4 method for signature 'HierarchicalPartition'
get_signatures(object, depth = max_depth(object),
    scale_rows = object[1]@scale_rows,
    anno = get_anno(object),
    anno_col = get_anno_col(object),
    show_column_names = FALSE,
    verbose = TRUE, plot = TRUE,
    silhouette_cutoff = 0.5,
    ...)

Arguments

object

a HierarchicalPartition-class object.

depth

depth of the hierarchy.

scale_rows

whether apply row scaling when making the heatmap.

anno

a data frame of annotations for the original matrix columns. By default it uses the annotations specified in hierarchical_partition.

anno_col

a list of colors (color is defined as a named vector) for the annotations. If anno is a data frame, anno_col should be a named list where names correspond to the column names in anno.

show_column_names

whether show column names in the heatmap.

verbose

whether to print messages.

plot

whether to make the plot.

silhouette_cutoff

cutoff for silhouette scores. Samples with values less than it are not used for finding signature rows. For selecting a proper silhouette cutoff, please refer to https://www.stat.berkeley.edu/~s133/Cluster2a.html#tth_tAb1.

...

other arguments

Details

The function calls get_signatures,ConsensusPartition-method to find signatures at each node of the partition hierarchy.

Value

A list of row indices where rows are significantly different between subgroups in at least one node.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

## Not run: 
data(cola_rh)
get_signatures(cola_rh)

## End(Not run)

[Package cola version 1.0.0 Index]