plot_hierarchies_line: Plot peptide intensities of protein as a function of the...

In wolski/prolfqua: Proteomics Label Free Quantification

Plot peptide intensities of protein as a function of the sample and factor

Description

Plot peptide intensities of protein as a function of the sample and factor

Usage

plot_hierarchies_line(
  res,
  proteinName,
  config,
  separate = FALSE,
  show.legend = FALSE
)

Arguments

res	data.frame
proteinName	title of plot
config	AnalysisConfiguration
separate	if heavy and light show in one plot or with separate y axis?

See Also

Other aggregation: INTERNAL_FUNCTIONS_BY_FAMILY, aggregate_intensity_topN(), estimate_intensity(), intensity_summary_by_hkeys(), medpolish_estimate(), medpolish_estimate_df(), medpolish_estimate_dfconfig(), medpolish_protein_estimates(), plot_estimate(), plot_hierarchies_add_quantline(), plot_hierarchies_line_df(), rlm_estimate(), rlm_estimate_dfconfig()

Other plotting: ContrastsPlotter, INTERNAL_FUNCTIONS_BY_FAMILY, UpSet_interaction_missing_stats(), UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), missingness_per_condition(), missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), plot_heatmap(), plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), plot_sample_correlation(), plot_screeplot()

Examples

istar <- sim_lfq_data_peptide_config()
config <- istar$config
analysis <- istar$data

xnested <- analysis |>
 dplyr::group_by_at(config$table$hierarchy_keys_depth()) |> tidyr::nest()

prolfqua::plot_hierarchies_line(xnested$data[[1]], xnested$protein_Id[[1]],config )

bb <- prolfqua_data('data_skylineSRM_HL_A')
conf <- bb$config_f()
analysis <- bb$analysis(bb$data, conf)

nest <- analysis |> dplyr::group_by(conf$table$hierarchy_keys_depth()) |> tidyr::nest()
prolfqua::plot_hierarchies_line(nest$data[[1]],
                                  "DUM",
                                  conf,
                                  separate = TRUE)
prolfqua::plot_hierarchies_line(nest$data[[1]],
"DUM",
conf,
separate = TRUE,
show.legend = TRUE)

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