plotProportionOfMitochondrialProteins: Plot proportion of mitochondrial proteins

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

Description

The function plotProportionOfMitochondrialProteins creates a plot of the proportion of mitochondrial proteins (obtained via calculateProportionOfMitochondrialProtein).

Usage

plotProportionOfMitochondrialProteins(proportion)

Arguments

proportion

numeric vector

Details

names(proportion) are taken as x-axis labels.

If there are no names for proportion (names(proportion) is NULL), names from 1:length(proportion) will be assigned to proportion.

Value

gg

Examples

set.seed(1)
## fake measured protein intensities and create matrix that stores 
## intensities
prot_vals <- runif(1000, min = 10000, max = 1000000)
prot <- matrix(prot_vals, ncol = 10, nrow = 100)

## fake some protein names and sample names
rownames(prot) <- paste("prot", seq_len(nrow(prot)), sep = "_")
colnames(prot) <- paste("sample", seq_len(ncol(prot)), sep = "_") 

## randomly assign 10 mitochondrial proteins to the matrix
inds_mito <- sample(seq_len(nrow(prot)), 10)
prot_mito <- c("MDH2", "OMA1", "NLN", "CS", "OPA1", "CSPG5", "SPATA9", "POLG", "RAB38", "NSD3")
rownames(prot)[inds_mito] <- prot_mito

prop_mito <- calculateProportionOfMitochondrialProteins(values = prot, id = "Symbol")
plotProportionOfMitochondrialProteins(proportion = prop_mito)

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