Plot PTM usage across all contrasts in multi-panel layout

Usage

n_to_c_usage_multicontrast(
  data_combined_diff,
  FDR_threshold = 0.05,
  fc_threshold = 0,
  impute_flag = "Imputed_Mean_moderated",
  protein_Id = "protein_Id",
  max_plots = NULL,
  include_proteins = NULL
)

Arguments

data_combined_diff: data frame with combined differential analysis results
FDR_threshold: FDR threshold for filtering significant sites (default 0.05)
fc_threshold: Fold change threshold for filtering (default 0)
impute_flag: Flag for imputed values (default "Imputed_Mean_moderated")
protein_Id: Column name for protein identifier (default "protein_Id")
max_plots: Maximum number of plots to generate (default NULL = no limit). If specified, only the first max_plots proteins will be plotted.
include_proteins: Character vector of protein IDs to always include in the output, regardless of max_plots limit (default NULL). These proteins will be added even if they exceed the max_plots limit.

Value

data frame with protein_Id, protein_length, n_contrasts, and multi-panel plot

Examples

# data(combined_diff_data)
# result <- n_to_c_usage_multicontrast(combined_diff_data,
#   max_plots = 50, include_proteins = c("Q64337"))
# print(result$plot[[1]])  # Display first protein's multi-contrast plot