plot_hierarchies_boxplot: plot peptides by factors and it's levels.

In wolski/prolfqua: Proteomics Label Free Quantification

plot peptides by factors and it's levels.

Description

plot peptides by factors and it's levels.

Usage

plot_hierarchies_boxplot(
  pdata,
  title,
  config,
  facet_grid_on = NULL,
  beeswarm = TRUE,
  show_mean = TRUE,
  pb
)

Arguments

pdata	data.frame
title	name to show
config	AnalysisConfiguration
facet_grid_on	on which variable to run facet_grid
beeswarm	use beeswarm default FALSE

Examples

bb <- prolfqua_data('data_skylineSRM_HL_A')
config <- bb$config_f()
analysis <- bb$analysis(bb$data, config)
data <- prolfqua::transform_work_intensity(analysis, config, log2)
res <- plot_hierarchies_boxplot_df(data, config)
res$boxplot[[1]]

hierarchy = config$table$hierarchy_keys_depth()
xnested <- data |> dplyr::group_by_at(hierarchy) |> tidyr::nest()
undebug(plot_hierarchies_boxplot)
p <- plot_hierarchies_boxplot(xnested$data[[1]], xnested$protein_Id[[1]],config, beeswarm = FALSE, show_mean=TRUE)
p <- plot_hierarchies_boxplot(xnested$data[[1]], xnested$protein_Id[[1]],config, beeswarm = TRUE)
p <- plot_hierarchies_boxplot(xnested$data[[1]], xnested$protein_Id[[1]],config, beeswarm = TRUE, facet_grid_on = "precursor_Id")
p

wolski/prolfqua documentation built on Dec. 4, 2024, 11:18 p.m.