get_signatures-HierarchicalPartition-method {cola} | R Documentation

## Get signatures rows

### Description

Get signatures rows

### Usage

    ## S4 method for signature 'HierarchicalPartition'
    get_signatures(object, merge_node = merge_node_param(),
        group_diff = object@param$group_diff,
        row_km = NULL, diff_method = "Ftest", fdr_cutoff = object@param$fdr_cutoff,
        scale_rows = object[1]@scale_rows,
        anno = get_anno(object),
        anno_col = get_anno_col(object),
        show_column_names = FALSE, column_names_gp = gpar(fontsize = 8),
        verbose = TRUE, plot = TRUE, seed = 888,
        ...)

### Arguments

`object` | a `HierarchicalPartition-class` object.
`merge_node` | Parameters to merge sub-dendrograms, see `merge_node_param`.
`group_diff` | Cutoff for the maximal difference between group means.
`row_km` | Number of groups for performing k-means clustering on rows. By default it is automatically selected.
`diff_method` | Methods to get rows which are significantly different between subgroups.
`fdr_cutoff` | Cutoff for FDR of the difference test between subgroups.
`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.
`column_names_gp` | Graphic parameters for column names.
`verbose` | whether to print messages.
`plot` | whether to make the plot.
`seed` | Random seed.
`...` | other arguments pass to `get_signatures,ConsensusPartition-method`.

### Details

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

### Value

A data frame with more than two columns:

`which_row`:

  row index corresponding to the original matrix.

`km`:

  the k-means groups if `row_km` is set.

other_columns:

  the mean value (depending rows are scaled or not) in each subgroup.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### Examples

    data(golub_cola_rh)
    tb = get_signatures(golub_cola_rh)
    head(tb)

[Package cola version 1.8.1 Index]