generates peptide level plots for all Proteins

generates peptide level plots for all Proteins

plot_hierarchies_boxplot_df(
  pdata,
  config,
  hierarchy = config$table$hierarchy_keys_depth(),
  facet_grid_on = NULL
)

Arguments

pdata

data.frame

config

AnalysisConfiguration

facet_grid_on

default NULL

hiearchy

e.g. protein_Id default hierarchy_keys_depth

See also

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

Examples

 istar <- sim_lfq_data_peptide_config(with_missing = FALSE)
#> creating sampleName from fileName column
#> completing cases
#> completing cases done
#> setup done
 res <- plot_hierarchies_boxplot_df(istar$data,istar$config)
 istar <- sim_lfq_data_peptide_config()
#> creating sampleName from fileName column
#> completing cases
#> completing cases done
#> setup done
 config <- istar$config
 analysis <- istar$data
 analysis <- analysis |>
   dplyr::filter(protein_Id %in% sample(protein_Id, 2))

 res <- plot_hierarchies_boxplot_df(analysis,config)
 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()`).

 res <- plot_hierarchies_boxplot_df(analysis,config,config$table$hierarchy_keys()[1])
 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()`).

 res <- plot_hierarchies_boxplot_df(analysis,config,
                                    config$table$hierarchy_keys()[1],
                                    facet_grid_on = config$table$hierarchy_keys()[2])
 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()`).

 res$boxplot[[2]]


 iostar <- sim_lfq_data_protein_config()
#> creating sampleName from fileName column
#> completing cases
#> completing cases done
#> setup done
 iostar$data <- iostar$data |>
   dplyr::filter(protein_Id %in% sample(protein_Id, 4))
 unique(iostar$data$protein_Id)
#> [1] "BEJI92~5282" "CGzoYe~2147" "SGIVBl~5782"

 res <- plot_hierarchies_boxplot_df(iostar$data,iostar$config)
 res$boxplot[[1]]
#> Warning: Removed 1 row containing non-finite outside the scale range (`stat_boxplot()`).
#> Warning: Removed 1 row containing non-finite outside the scale range (`stat_summary()`).
#> Warning: Removed 1 row containing non-finite outside the scale range (`stat_summary()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`position_quasirandom()`).

 res <- plot_hierarchies_boxplot_df(iostar$data,iostar$config,
                                    iostar$config$table$hierarchy_keys()[1])