plot_hierarchies_line_df: Generates peptide level plots for all proteins

In wolski/prolfqua: Proteomics Label Free Quantification

Generates peptide level plots for all proteins

Description

Generates peptide level plots for all proteins

Usage

plot_hierarchies_line_df(pdata, config, show.legend = FALSE)

Arguments

pdata	data.frame
config	AnalysisConfiguration

See Also

plot_hierarchies_line

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(), 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(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), plot_sample_correlation(), plot_screeplot()

Examples

istar <- prolfqua_data('data_ionstar')$normalized()

istar_data <- istar$data |> dplyr::filter(protein_Id %in% sample(protein_Id, 20))
config <-  old2new(istar$config)

config$table$is_response_transformed <- FALSE
#debug(plot_hierarchies_line_df)
res <- plot_hierarchies_line_df(istar_data, config)

config$table$is_response_transformed <- TRUE
res <- plot_hierarchies_line_df(istar_data, config)

istar <- prolfqua_data('data_ionstar')$filtered()
istar_data <- istar$data |> dplyr::filter(protein_Id %in% sample(protein_Id, 20))
config <-  old2new(istar$config)
res <- plot_hierarchies_line_df(istar_data, config)
config$table$is_response_transformed
config$table$is_response_transformed <- TRUE
res <- plot_hierarchies_line_df(istar_data, config)
config$table$is_response_transformed

#TODO make it work for other hiearachy levels.
config$table$hierarchyDepth = 2
#res <- plot_hierarchies_line_df(resDataStart, config)

wolski/prolfqua documentation built on May 12, 2024, 10:16 p.m.