plot_ContUserScore: Plot Andromeda score distribution of contaminant peptide vs....

View source: R/fcn_plots.R

plot_ContUserScoreR Documentation

Plot Andromeda score distribution of contaminant peptide vs. matrix peptides.


The data is expected to be an ECDF already, x being the Andromeda score, y being the culmulative probability. The Score is the probability of a Kolm.-Smirnoff test that the contaminant scores are larger (i.e. large p-values indicate true contamination). You will only see this plot if the but high-scoring contaminant peptides, which would erroneously give you a large p-value and make you believe your sample is contaminated although that's not the case.


plot_ContUserScore(data, raw.file, score)



A data.frame with columns 'x', 'y', 'condition'


Name of Raw file for which the data is displayed (will become part of the plot title)


Score of how distinct the distributions are (will become part of the title)


GGplot object


 data = data.frame(x = 10:60,
                   y = c(seq(0,1,length=51), seq(0.1, 1, length=51)), 
                   condition = rep(c("sample","contaminant"), each=51))
 plot_ContUserScore(data, 'test file', 0.96)

PTXQC documentation built on July 26, 2023, 5:27 p.m.