EMDomics (version 2.2.2)

plot_cvm_density: Plot distributions and CVM score for a gene.

Description

The data for the specified gene is retrieved from cvmobj$data. outcomes is used to divide the data into distributions for each group, which are then visualized as density distributions. The calculated CVM score for the specified gene is displayed in the plot title.

Usage

plot_cvm_density(cvmobj, gene_name)

Arguments

cvmobj

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

gene_name

The gene to visualize. The name should be defined as a row name in cvmobj$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_cvm_density(results, "gene5")