plot_heatmap {musicatk} | R Documentation

## Plot heatmaps using the exposures matrix

### Description

The exposures for different signatures can be visualized using a heatmap with this function. Heatmaps make it easier to visualize the data by representing the magbitude of exposure values as color in 2-dimensions. The variation in color intensity can help see if the exposures are clustered or how they vary over space. Exposures can be normalized by providing the `proportional` argument. Column annotations can also be seen by passing the `col_annot` argument.

### Usage

    plot_heatmap(
      res_annot,
      proportional = FALSE,
      show_column_names = FALSE,
      show_row_names = TRUE,
      scale = TRUE,
      subset_tumor = NULL,
      subset_signatures = NULL,
      annotation = NULL,
      ...
    )

### Arguments

`res_annot` | A `musica_result` object generated by a mutational discovery or prediction tool.
`proportional` | If `TRUE`, then the exposures will be normalized to between 0 and 1 by dividing by the total number of counts for each sample. Default `FALSE`.
`show_column_names` | Boolean check. If `True`, column names are shown. Otherwise, they aren't. Default `FALSE`
`show_row_names` | Boolean check. If `True`, row names are shown. Otherwise, they aren't. Default `FALSE`
`scale` | Boolean check. If `True`, values are scaled by z-score. Otherwise, they aren't. Default `TRUE`
`subset_tumor` | Users can specify certain tumor types on which they want to subset the exposure matrix for plotting the heatmap.
`subset_signatures` | Users can specify certain signatures on which they want to subset the exposure matrix plotting the heatmap.
`annotation` | Users have the option of plotting the exposure matrix based on their given annotation like Tumor_Subtypes or age. Error given if the user given annotation doesn't exist in the res_annot annotation object.
`...` | Ellipsis used for passing any arguments directly to the ComplexHeatmap's heatmap function.

### Value

Generates a heatmap for using the exposure matrix.

### Examples

    data(res_annot)
    plot_heatmap(res_annot = res_annot, proportional = TRUE, scale = TRUE,
    annotation = "Tumor_Subtypes")

[Package musicatk version 1.2.0 Index]