complex_heatmap_exposures {YAPSA} | R Documentation

## Heatmap to cluster the PIDs on their signature exposures (ComplexHeatmap)

### Description

The PIDs are clustered according to their signature exposures. uses package ComplexHeatmap by Zuguang Gu. This function calls:

- `rowAnnotation`,

- `HeatmapAnnotation` and

- `Heatmap`

### Usage

    complex_heatmap_exposures(
      in_exposures_df,
      in_subgroups_df,
      in_signatures_ind_df,
      in_data_type = "norm exposures",
      in_method = "manhattan",
      in_subgroup_column = "subgroup",
      in_subgroup_colour_column = NULL,
      in_palette = colorRamp2(c(0, 0.2, 0.4, 0.6), c("white", "yellow", "orange", "red")),
      in_cutoff = 0,
      in_filename = NULL,
      in_column_anno_borders = FALSE,
      in_row_anno_borders = 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_signatures_ind_df` | A data frame containing meta information about the signatures, especially the asserted colour
`in_data_type` | Title in the figure
`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_subgroup_colour_column` | Indicates the name of the column in which the colour information for subgroups is encoded in `in_subgroups_df`. If NULL, a rainbow palette is used instead.
`in_palette` | Palette with colours for the heatmap. Default is `colorRamp2(c(0, 0.2, 0.4, 0.6), c('white','yellow','orange','red'))`
`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 heatmap. If none is specified, the figure will be plotted to the running environment.
`in_column_anno_borders` | Whether or not to draw separating lines between the fields in the annotation
`in_row_anno_borders` | Whether or not to draw separating lines between the fields in the annotation

### Details

It might be necessary to install the newest version of the development branch of the packages circlize and ComplexHeatmap by Zuguang Gu: `devtools::install_github("jokergoo/circlize")` and `devtools::install_github("jokergoo/ComplexHeatmap")`

### Value

The function doesn't return any value.

### See Also

`Heatmap`

### Examples

     data(lymphoma_cohort_LCD_results)
     complex_heatmap_exposures(
       rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df,
       COSMIC_subgroups_df,
       chosen_signatures_indices_df,
       in_data_type="norm exposures",
       in_subgroup_colour_column="col",
       in_method="manhattan",
       in_subgroup_column="subgroup")

[Package YAPSA version 1.20.1 Index]