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

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 1.18.0 Index]