mdsArrange: mdsArrange

In abc-igmm/transcripTools: Collection of functions for analysing gene expression data

Description

A function to take a matrix/dataframe of gene expression data and return a dataframe suitable for plotting as an MDS plot with ggplot2

Usage

mdsArrange(d, isAlreadyScaled = FALSE)

Arguments

d	is a dataframe of gene expression data
isAlreadyScaled	Logical value for whether d is already scaled

Value

A dataframe compatible with ggplot2

Examples

#Using the NKI dataset
library(breastCancerNKI)
library(Biobase)
data(nki)
mtx <- exprs(nki)

#Calculate PCs 1 & 2
mds_dfr <- mdsArrange(d = mtx, isAlreadyScaled = TRUE)
#Merge with phenotypic data for plotting
mds_mrg <- merge(mds_dfr, pData(nki), by = 0)

#Plot MDS and colour by estrogen receptor positivity
library(ggplot2)
ggplot(mds_mrg, aes(x = x, y  = y, colour = as.factor(er))) + 
    geom_point()

abc-igmm/transcripTools documentation built on May 20, 2019, 3:05 p.m.