top_rows_heatmap-matrix-method {cola} | R Documentation

## Heatmap of top rows from different top-value methods

### Description

Heatmap of top rows from different top-value methods

### Usage

    ## S4 method for signature 'matrix'
    top_rows_heatmap(object, all_top_value_list = NULL,
        top_value_method = all_top_value_methods(),
        bottom_annotation = NULL,
        top_n = round(0.25*nrow(object)), scale_rows = TRUE, ...)

### Arguments

`object` | A numeric matrix.
`all_top_value_list` | Top-values that have already been calculated from the matrix. If it is `NULL` the values are calculated by methods in `top_value_method` argument.
`top_value_method` | Methods defined in `all_top_value_methods`.
`bottom_annotation` | A `HeatmapAnnotation-class` object.
`top_n` | Number of top rows to show in the heatmap.
`scale_rows` | Whether to scale rows.
`...` | Pass to `Heatmap`.

### Details

The function makes heatmaps where the rows are scaled (or not scaled) for the top n rows from different top-value methods.

The top n rows are used for subgroup classification in cola analysis, so the heatmaps show which top-value method gives better candidate rows for the classification.

### Value

No value is returned.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### Examples

    set.seed(123)
    mat = matrix(rnorm(1000), nrow = 100)
    top_rows_heatmap(mat, top_n = 25)

[Package cola version 1.8.1 Index]