plotSampleScores: Plot the contamination scores of samples

In tnaake/apoptosisQuantification: Assessment of apoptosis and necroptosus unsing proteomics

Description

The function plotSampleScores creates a barplot or boxplot that visualizes the contamination score values obtained by scoreSamples.

Usage

plotSampleScores(scores)

Arguments

scores

tibble

Details

The function takes the argument scores that can be created via scoreSamples.

Value

gg

Examples

library(SummarizedExperiment)
library(tibble)

f <- system.file("protein_datasets/tanzer2020.RDS", 
    package = "apoptosisQuantification")
tanzer2020 <- readRDS(f)
prot <- assay(tanzer2020)

## use the intensities to calculate scores
scores <- scoreSamples(values = prot, contamination = "apoptosis",fc = 2, n = 1, n_perm = 100)
scores$treatment <- tanzer2020$treatment
plotSampleScores(scores = scores) +
    ggplot2::facet_wrap(~ treatment, scales = "free_x") +
    ggplot2::theme(legend.position = "none")

## use the intensities to calculate scores
scores <- scoreSamples(values = prot, contamination = "necroptosis", n_perm = 100)
scores$treatment <- tanzer2020$treatment
plotSampleScores(scores = scores) +
    ggplot2::facet_wrap(~ treatment, scales = "free_x") +
    ggplot2::theme(legend.position = "none")

tnaake/apoptosisQuantification documentation built on Feb. 20, 2022, 5:37 p.m.