plot_emd_density: Plot distributions and EMD score for a gene.

In schmolze/EMDomics-devel: Earth Mover's Distance for Differential Analysis of Genomics Data

Description

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

Usage

plot_emd_density(emdobj, gene_name)

Arguments

emdobj	An EMDomics object, typically returned via a call to calculate_emd.
gene_name	The gene to visualize. The name should be defined as a row name in emdobj$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_emd_density(results, "gene5")

schmolze/EMDomics-devel documentation built on May 29, 2019, 3:42 p.m.