Line plot of number of true and false positives when applying different logFC thresholds

Usage

plot_logFC_thresholds_spiked(
  se,
  de_res,
  condition,
  ain = NULL,
  comparisons = NULL,
  nrow = 2,
  alpha = 0.05
)

Arguments

se: SummarizedExperiment containing all necessary information of the proteomics data set
de_res: data table resulting of run_DE
condition: column name of condition (if NULL, condition saved in SummarizedExperiment will be taken)
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)
nrow: number of rows for facet wrap
alpha: threshold for adjusted p-values

Value

list of ggplot objects

Examples

data(spike_in_se)
data(spike_in_de_res)
plot_logFC_thresholds_spiked(spike_in_se, spike_in_de_res,
                             condition = "Condition", ain = NULL,
                             comparisons = NULL, nrow = 2, alpha = 0.05)
#> All comparisons of de_res will be visualized.
#> All normalization methods of de_res will be visualized.
#> $TP

#> 
#> $FP

#>