plotECDF: Plot empirical cumulative distribution function of loading...

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

Description

The function plotECDF creates an empirical cumulative distribution function (ECDF) plot of the loadings distribution of marker and non-markers.

Usage

plotECDF(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 plotECDF 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
prot <- assay(tanzer2020)
markers <- readMarkers(type = "apoptosis")

## plot the distribution as ECDF
plotECDF(values = prot, markers = markers, PC = "PC1")

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