get_signatures-HierarchicalPartition-method {cola} | R Documentation |
Get signatures rows
## 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, ...)
object |
a |
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 |
anno_col |
a list of colors (color is defined as a named vector) for the annotations. If |
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 |
The function calls get_signatures,ConsensusPartition-method
to find signatures at
each node of the partition hierarchy.
A list of row indices where rows are significantly different between subgroups in at least one node.
Zuguang Gu <z.gu@dkfz.de>
## Not run: data(cola_rh) get_signatures(cola_rh) ## End(Not run)