visualize intensity distributions

visualize intensity distributions

visualize intensity distributions

plot_intensity_distribution_violin(pdata, config)

plot_intensity_distribution_density(pdata, config, legend = TRUE)

Arguments

pdata

data.frame

config

AnalysisConfiguration

legend

do not show legend

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_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), plot_hierarchies_line(), plot_hierarchies_line_df(), plot_pca(), plot_raster(), plot_sample_correlation(), plot_screeplot()

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_hierarchies_line_df(), plot_pca(), plot_raster(), plot_sample_correlation(), plot_screeplot()

Examples

istar <-sim_lfq_data_peptide_config()
#> creating sampleName from fileName column
#> Warning: no nr_children column specified in the data, adding column nr_children and setting to 1.
#> completing cases

config <- istar$config
analysis <- istar$data

plot_intensity_distribution_violin(analysis, config)
#> Warning: Removed 36 rows containing non-finite outside the scale range
#> (`stat_ydensity()`).
#> Warning: Removed 36 rows containing non-finite outside the scale range
#> (`stat_summary()`).

analysis <- transform_work_intensity(analysis, config, log2)
#> Column added : log2_abundance
plot_intensity_distribution_violin(analysis, config)
#> Warning: Removed 36 rows containing non-finite outside the scale range
#> (`stat_ydensity()`).
#> Warning: Removed 36 rows containing non-finite outside the scale range
#> (`stat_summary()`).



istar <-sim_lfq_data_peptide_config()
#> creating sampleName from fileName column
#> Warning: no nr_children column specified in the data, adding column nr_children and setting to 1.
#> completing cases

config <- istar$config
analysis <- istar$data
plot_intensity_distribution_density(analysis, config)
#> Warning: Removed 36 rows containing non-finite outside the scale range
#> (`stat_density()`).

analysis <- transform_work_intensity(analysis, config, log2)
#> Column added : log2_abundance
plot_intensity_distribution_density(analysis, config)
#> Warning: Removed 36 rows containing non-finite outside the scale range
#> (`stat_density()`).