heatmapTable {GenomicSuperSignature} | R Documentation

## Validation result in heatmap format

### Description

This function subsets `validate` outputs with different criteria and visualize it in a heatmap-like table.

### Usage

    heatmapTable(
      val_all,
      ind = NULL,
      num.out = 5,
      scoreCutoff = NULL,
      swCutoff = NULL,
      clsizeCutoff = NULL,
      breaks = c(0, 0.5, 1),
      colors = c("white", "white smoke", "red"),
      column_title = NULL,
      row_title = NULL,
      whichPC = NULL,
      ...
    )

### Arguments

`val_all` | An output matrix from `validate` function with the parameter `level = "max"`. Subset of this matrix is plotted as a heatmap using `Heatmap`
`ind` | An integer vector. If this parameter is provided, the other parameters, `num.out, scoreCutoff, swCutoff, clsizeCutoff` will be ignored and the heatmap table containing only the provided index will be printed.
`num.out` | A number of highly validated RAVs to output. Default is 5. If any of the cutoff parameters are provided, `num.out` or the number of filtered RAVs, whichever smaller, will be chosen.
`scoreCutoff` | A numeric value for the minimum correlation. If `val_all` input is from multiple studies, the default is 0.7 and this is the only cutoff criteria considered: `swCutoff` and `clsizeCutoff` will be ignored.
`swCutoff` | A numeric value for the minimum average silhouette width.
`clsizeCutoff` | A integer value for the minimum cluster size.
`breaks` | A numeric vector of length 3. Number represents the values assigned to three colors. Default is `c(0, 0.5, 1)`.
`colors` | A character vector of length 3. Each represents the color assigned to three breaks. Default is `c("white", "white smoke", "red")`.
`column_title` | A character string. Provide the column title.
`row_title` | A character string. Provide the row title.
`whichPC` | An integer value between 1 and 8. PC number of your data to check the validated signatures with. Under the default (`NULL`), it outputs top scored signatures with any PC of your data.
`...` | any additional argument for `Heatmap`

### Value

A heatmap displaying the subset of the validation result that met the given cutoff criteria. If `val_all` input is from a single dataset, the output heatmap will contain both score and average silhouette width for each cluster.

If `val_all` input is from multiple studies, the output heatmap's rows will represent each study and the columns will be RAVs, which meet `scoreCutoff` for any of the input studies.

### Examples

    data(miniRAVmodel)
    library(bcellViper)
    data(bcellViper)
    val_all <- validate(dset, miniRAVmodel)
    heatmapTable(val_all, swCutoff = 0)

[Package GenomicSuperSignature version 1.0.1 Index]