plot_SMC {YAPSA} | R Documentation

## Plot results of the Stratification of a Mutational Catalogue

### Description

Plot a big composite figure with 3 columns: in the left column the per-PID absolute exposures will be shown, in the middle column the per_PID relative or normalized exposures will be shown, in the right column the cohort-wide exposures are shown (averaged over PIDs).

### Usage

    plot_SMC(
      number_of_strata,
      output_path,
      decomposition_method,
      number_of_sigs,
      name_list,
      exposures_strata_list,
      this_signatures_ind_df,
      this_subgroups_df,
      in_strata_order_ind,
      exposures_both_rel_df_list,
      cohort_method_flag,
      fig_width = 1200,
      fig_height = 900,
      fig_type = "png",
      in_label_orientation = "turn",
      this_sum_ind = NULL
    )

### Arguments

`number_of_strata` | Number of strata as deduced from `link{SMC}`
`output_path` | Path to file where the results are going to be stored. If NULL, the results will be plotted to the running environment.
`decomposition_method` | String for the filename of the generated barplot.
`number_of_sigs` | Number of signatures
`name_list` | Names of the contructed strata.
`exposures_strata_list` | The list of `s` strata specific exposures Hi, all are numerical data frames with `l` rows and `m` columns, `l` being the number of signatures and `m` being the number of samples
`this_signatures_ind_df` | A data frame containing meta information about the signatures
`this_subgroups_df` | A data frame indicating which PID (patient or sample identifyier) belongs to which subgroup
`in_strata_order_ind` | Index vector defining reordering of the strata
`exposures_both_rel_df_list` | A list of `s` strata specific cohortwide (i.e. averaged over cohort) normalized exposures
`cohort_method_flag` | Either or several of `c("all_PIDs","cohort","norm_PIDs")`, representing alternative ways to average over the cohort.
`fig_width` | Width of the figure to be plotted
`fig_height` | Height of the figure to be plotted
`fig_type` | png or pdf
`in_label_orientation` | Whether or not to turn the labels on the x-axis.
`this_sum_ind` | Optional set of indices for reordering the PIDs

### Value

The function doesn't return any value.

### Examples

    NULL

[Package YAPSA version 1.18.0 Index]