hclust_exposures {YAPSA} | R Documentation

## Cluster the PIDs according to their signature exposures

### Description

The PIDs are clustered according to their signature exposures by calling first creating a distance matrix:

- `dist`, then

- `hclust` and then

- `labels_colors` to colour the labels (the text) of the leaves in the dendrogram.

Typically one colour per subgroup.

### Usage

    hclust_exposures(
      in_exposures_df,
      in_subgroups_df,
      in_method = "manhattan",
      in_subgroup_column = "subgroup",
      in_palette = NULL,
      in_cutoff = 0,
      in_filename = NULL,
      in_shift_factor = 0.3,
      in_cex = 0.2,
      in_title = "",
      in_plot_flag = FALSE
    )

### Arguments

`in_exposures_df` | Numerical data frame encoding the exposures `H`, i.e. which signature contributes how much to which PID (patient identifier or sample).
`in_subgroups_df` | A data frame indicating which PID (patient or sample identifyier) belongs to which subgroup
`in_method` | Method of the clustering to be supplied to `dist`. Can be either of: `euclidean`, `maximum`, `manhattan`, `canberra`, `binary` or `minkowski`
`in_subgroup_column` | Indicates the name of the column in which the subgroup information is encoded in `in_subgroups_df`
`in_palette` | Palette with colours or colour codes for the labels (the text) of the leaves in the dendrogram. Typically one colour per subgroup. If none is specified, a rainbow palette of the length of the number of subgroups will be used as default.
`in_cutoff` | A numeric value less than 1. Signatures from within `W` with an overall exposure less than `in_cutoff` will be discarded for the clustering.
`in_filename` | A path to save the dendrogram. If none is specified, the figure will be plotted to the running environment.
`in_shift_factor` | Graphical parameter to adjust figure to be created
`in_cex` | Graphical parameter to adjust figure to be created
`in_title` | Title in the figure to be created under `in_filename`
`in_plot_flag` | Whether or not to display the dendrogram

### Value

A list with entries `hclust` and `dendrogram`.

- `hclust`: The object created by `hclust`

- `dendrogram`: The above object wrapped in `as.dendrogram`

### See Also

`hclust`

`dist`

`labels_colors`

### Examples

     data(lymphoma_cohort_LCD_results)
     hclust_exposures(rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df,
                      COSMIC_subgroups_df,
                      in_method="manhattan",
                      in_subgroup_column="subgroup")

[Package YAPSA version 1.18.0 Index]