plot_emdperms: Plot histogram of EMD scores calculated via random...

In EMDomics: Earth Mover's Distance for Differential Analysis of Genomics Data

Description

The permuted EMD scores stored in emdobj$emd.perm are plotted as a histogram.

Usage

plot_emdperms(emdobj)

Arguments

emdobj

An EMDomics object, typically returned via a call to calculate_emd.

Value

A ggplot object is returned. If the value is not assigned, a plot will be drawn.

See Also

calculate_emd ggplot

Examples

# 100 genes, 100 samples
dat <- matrix(rnorm(10000), nrow=100, ncol=100)
rownames(dat) <- paste("gene", 1:100, sep="")
colnames(dat) <- paste("sample", 1:100, sep="")

# "A": first 50 samples; "B": next 30 samples; "C": final 20 samples
outcomes <- c(rep("A",50), rep("B",30), rep("C",20))
names(outcomes) <- colnames(dat)

results <- calculate_emd(dat, outcomes, nperm=10, parallel=FALSE)
plot_emdperms(results)

EMDomics documentation built on Nov. 8, 2020, 5:30 p.m.