annotation_exposures_list_barplot {YAPSA} | R Documentation

## Plot the exposures of a cohort with different layers of annotation for SNV and INDEL signatures

### Description

The exposures `H`, determined by NMF or by `LCD`, are displayed as a stacked barplot by calling `Heatmap`. The x-axis displays the PIDs (patient identifier or sample), the y-axis the counts attributed to the different signatures with their respective colours per PID. It is analogous to `plot_exposures`. As many layers of information as desired can be added via an annotation data frame. The annotation data is handled in a way similar to `annotation_heatmap_exposures`. In comparison to `annotation_exposures_barplot` allows this function to deal with a list of differn signature and mutation types. This function calls:

- `rowAnnotation`,

- `HeatmapAnnotation` and

- `Heatmap`

### Usage

    annotation_exposures_list_barplot(
      in_exposures_list,
      in_signatures_ind_list,
      in_subgroups_list,
      in_annotation_list,
      ylab = NULL,
      title = "",
      in_indel_sigs = FALSE,
      in_labels = FALSE,
      in_barplot_borders = TRUE,
      in_column_anno_borders = FALSE,
      in_annotation_legend_side = "right",
      in_padding = unit(c(2, 20, 2, 2), "mm"),
      in_annotation = NULL
    )

### Arguments

`in_exposures_list` | A list of numerical data frame encoding the exposures `H` of different signature types, i.e. which signature contributes how much to which PID (patient identifier or sample).
`in_signatures_ind_list` | A list of data frame containing meta information about the each signature type individually
`in_subgroups_list` | A list of data frame indicating of each siganture type which PID (patient or sample identifyier) belongs to which subgroup
`in_annotation_list` | A list data frame indicating which PID (patient or sample identifyier) belongs to which subgroup for all layers of annotation and a list indicating colour attributions for all layers of annotation for each siganture type individually
`ylab` | String indicating the column name in `in_subgroups_df` to take the subgroup information from.
`title` | Title for the plot to be created.
`in_indel_sigs` | Tag which is default FALSE when whole genome data are analysed the tag will be TRUE
`in_labels` | Whether or not to show the names of the samples.
`in_barplot_borders` | Whether or not to show border lines in barplot
`in_column_anno_borders` | Whether or not to draw separating lines between the fields in the annotation
`in_annotation_legend_side` | Where to put the legends of the annotation df, default is right.
`in_padding` | Parameter passed on to function `draw`
`in_annotation` | A full annotation object may also be provided by the educated user.

### 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")`

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

`HeatmapAnnotation`

`Heatmap`

`decorate_heatmap_body`

`annotation_heatmap_exposures`

`plot_exposures`

### Examples

     NULL

[Package YAPSA version 1.18.0 Index]