exposures_barplot: Wrapper for enhanced_barplot

In slw287r/yapsa: Yet Another Package for Signature Analysis

Description

Wrapper for enhanced_barplot

Usage

exposures_barplot(
  in_exposures_df,
  in_signatures_ind_df = NULL,
  in_subgroups_df = NULL,
  in_sum_ind = NULL,
  in_subgroups.field = "subgroup",
  in_title = "",
  in_labels = TRUE,
  in_show_subgroups = TRUE,
  ylab = NULL,
  in_barplot_borders = TRUE,
  in_column_anno_borders = FALSE
)

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. If NULL, the colour information for the signatures is taken from a rainbow palette.
in_subgroups_df	A data frame indicating which PID (patient or sample identifyier) belongs to which subgroup. If NULL, it is assumed that all PIDs belong to one common subgroup. The colour coding for the default subgroup is red.
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
ylab	Label of the y-axis on the plot to be generate
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

Value

The generated barplot - a ggplot2 plot

Examples

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

slw287r/yapsa documentation built on June 7, 2020, 12:46 a.m.