plot_cvmperms: Plot histogram of CVM scores calculated via random...

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

Description

The permuted CVM scores stored in cvmobj$cvm.perm are plotted as a histogram.

Usage

plot_cvmperms(cvmobj)

Arguments

cvmobj

An CVMomics object, typically returned via a call to calculate_cvm.

Value

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

See Also

calculate_cvm 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_cvm(dat, outcomes, nperm=10, parallel=FALSE)
plot_cvmperms(results)

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