plot_exposures {YAPSA} | R Documentation

## Plot the exposures of a cohort

### Description

`plot_exposures`: The exposures `H`, determined by NMF or by `LCD`, are displayed as a stacked barplot by calling

- `geom_bar` and optionally

- `geom_text`.

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. Is called by `plot_relative_exposures`.

`plot_relative_exposures`: Plot the relative or normalized exposures of a cohort. This function first normalizes its input and then sends the normalized data to `plot_exposures`.

### Usage

    plot_exposures(
      in_exposures_df,
      in_signatures_ind_df,
      in_subgroups_df = NULL,
      in_sum_ind = NULL,
      in_subgroups.field = "subgroup",
      in_title = "",
      in_labels = TRUE,
      in_show_subgroups = TRUE,
      legend_height = 10
    )

    plot_relative_exposures(
      in_exposures_df,
      in_signatures_ind_df,
      in_subgroups_df,
      in_sum_ind = NULL,
      in_subgroups.field = "subgroup",
      in_title = "",
      in_labels = TRUE,
      in_show_subgroups = TRUE
    )

### 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_signatures_ind_df` | A data frame containing meta information about the signatures
`in_subgroups_df` | A data frame indicating which PID (patient or sample identifyier) belongs to which subgroup
`in_sum_ind` | Index vector influencing the order in which the PIDs are going to be displayed
`in_subgroups.field` | String indicating the column name in `in_subgroups_df` to take the subgroup information from.
`in_title` | Title for the plot to be created.
`in_labels` | Flag, if `TRUE` the PIDs are displayed on the x-axis
`in_show_subgroups` | Flag, if `TRUE` then PIDs are grouped by subgroups
`legend_height` | How many signatures should be displayed in one column together at most.

### Value

The generated barplot - a ggplot2 plot

### See Also

`LCD`

`geom_bar`

`geom_text`

### Examples

     data(lymphoma_cohort_LCD_results)
     plot_exposures(lymphoma_Nature2013_COSMIC_cutoff_exposures_df,
                    chosen_signatures_indices_df,
                    COSMIC_subgroups_df)

     data(lymphoma_cohort_LCD_results)
     plot_relative_exposures(lymphoma_Nature2013_COSMIC_cutoff_exposures_df,
                             chosen_signatures_indices_df,
                             COSMIC_subgroups_df)

[Package YAPSA version 1.16.0 Index]