plotViolin: Plot the distribution of loading values via a violin plot

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

Description

The function plotViolin creates violin plots of the loadings distribution of marker and non-markers.

Usage

plotViolin(values, markers, PC = "PC1")

Arguments

values	matrix or data.frame
markers	tbl
PC	character, has to be in the format "PC1", "PC2", "PC3", ..., the specification of multiple principal components is possible and the length of loadings vectors will be calculated using these principal components

Details

The function plotViolin takes as input a tibble (tbl) that stores the loading values in the column "value" and the information on marker/non-marker in the column "type".

Value

gg

Examples

library(MatrixQCvis)
library(SummarizedExperiment)

## load data set of Tanzer et al. (2020)
## source: https://www.ebi.ac.uk/pride/archive/projects/PXD014966
f <- system.file("protein_datasets/tanzer2020.RDS",
    package = "apoptosisQuantification")
tanzer2020 <- readRDS(f)

## get loadings of markers and of the complete data set
values <- assay(tanzer2020)
markers <- readMarkers(type = "apoptosis", fc = 2, n = 1)

plotViolin(values = values, markers = markers, PC = "PC1")

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