plot_exposures: Plot the exposures of a cohort

In eilslabs/YAPSA: Yet Another Package for Signature Analysis

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)

eilslabs/YAPSA documentation built on May 16, 2019, 1:23 a.m.