Boxplot of p-values of spike-in and background proteins for specific normalization methods and comparisons. The ground truth (calculated based on the concentrations of the spike-ins) is shown as a horizontal line.

Boxplot of p-values of spike-in and background proteins for specific normalization methods and comparisons. The ground truth (calculated based on the concentrations of the spike-ins) is shown as a horizontal line.

Usage

plot_pvalues_spiked(se, de_res, ain = NULL, comparisons = NULL)

Arguments

se

SummarizedExperiment containing all necessary information of the proteomics data set

de_res

data table resulting of run_DE

ain

Vector of strings of normalization methods to visualize (must be valid normalization methods saved in stats)

comparisons

Vector of comparisons (must be valid comparisons saved in stats)

Value

ggplot object

Examples

data(spike_in_se)
data(spike_in_de_res)
plot_pvalues_spiked(spike_in_se, spike_in_de_res, ain = NULL,
                    comparisons = NULL)
#> All comparisons of de_res will be visualized.
#> All normalization methods of de_res will be visualized.
#> Warning: Removed 2225 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).