Generates peptide level plots for all proteins

Generates peptide level plots for all proteins

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_heatmap_cor_iheatmap(), 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 <- sim_lfq_data_peptide_config()
#> creating sampleName from fileName column
#> completing cases
#> completing cases done
#> setup done

istar$config$table$is_response_transformed <- FALSE
res <- plot_hierarchies_line_df(istar$data, istar$config)
res[[1]]
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_line()`).

istar$config$table$is_response_transformed <- TRUE
res <- plot_hierarchies_line_df(istar$data, istar$config)
res[[2]]
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_point()`).


#TODO make it work for other hiearachy levels.