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generates peptide level plots for all Proteins

Source: R/tidyMS_plotting.R
plot_hierarchies_boxplot_df.Rd

generates peptide level plots for all Proteins

Usage

plot_hierarchies_boxplot_df(
  pdata,
  lfqdata,
  hierarchy = lfqdata$relevant_hierarchy_keys(),
  facet_grid_on = NULL
)

Arguments

pdata

data.frame

lfqdata

LFQData object

hierarchy

e.g. protein_Id default relevant_hierarchy_keys

facet_grid_on

default NULL

See also

Other plotting: ContrastsPlotter, INTERNAL_FUNCTIONS_BY_FAMILY, medpolish_estimate_df(), missigness_histogram(), missingness_per_condition(), missingness_per_condition_cumsum(), plot_estimate(), plot_heatmap(), plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_line(), plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_na_heatmap(), plot_pca(), plot_raster(), plot_sample_correlation(), upset_interaction_missing_stats(), upset_missing_stats()

Examples


istar <- sim_lfq_data_peptide_config()
#> creating sampleName from file_name column
#> completing cases
#> completing cases done
#> setup done
lfq <- LFQData$new(istar$data, istar$config)
res <- plot_hierarchies_boxplot_df(lfq$data_long(), lfq)
res$boxplot[[1]]
#> Warning: Removed 7 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).
#> Warning: Removed 7 rows containing non-finite outside the scale range
#> (`stat_summary()`).
#> Warning: Removed 7 rows containing non-finite outside the scale range
#> (`stat_summary()`).
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`position_quasirandom()`).


lfq2 <- LFQData$new(
  istar$data |> dplyr::filter(protein_Id %in% sample(protein_Id, 2)),
  istar$config)
res <- plot_hierarchies_boxplot_df(lfq2$data_long(), lfq2)
res$boxplot[[1]]
#> Warning: Removed 8 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).
#> Warning: Removed 8 rows containing non-finite outside the scale range
#> (`stat_summary()`).
#> Warning: Removed 8 rows containing non-finite outside the scale range
#> (`stat_summary()`).
#> Warning: Removed 8 rows containing missing values or values outside the scale range
#> (`position_quasirandom()`).