enrichBarplot: Barplot of enriched and depleted annotations.

In coRdon: Codon Usage Analysis and Prediction of Gene Expressivity

Description

Make a barplot of enriched annotations. Bars' heights represent values of the chosen enrichment statistic (c("enrich","M","A")), and the colours represent the p values (c("pvals", "padj")).

Usage

enrichBarplot(x, variable, pvalue = "pvals", siglev = numeric())

## S4 method for signature 'list'
enrichBarplot(x, variable, pvalue = "pvals",
  siglev = numeric())

## S4 method for signature 'AnnotatedDataFrame'
enrichBarplot(x, variable,
  pvalue = "pvals", siglev = numeric())

Arguments

x	AnnotatedDataFrame object, or a list of those.
variable	Character, indicating the statistic values to be used for plotting, must be one of c("enrich","M","A").
pvalue	Character, one of c("pvals", "padj").
siglev	Numeric, significance level to be used for plotting.

Value

A ggplot object.

Examples

require(ggplot2)

HD59_PATHWAYS
enrichBarplot(HD59_PATHWAYS, variable = "M",
              pvalue = "padj", siglev = 0.01) +
   labs(y = "pathway count\nlog ratios", x = "KEGG Pathway")

x <- list(disease = LD94_PATHWAYS, healthy = HD59_PATHWAYS)
enrichBarplot(x, variable = "enrich", pvalue = "padj", siglev = 0.01) +
    labs(y = "relative enrichment", x = "KEGG Pathway")

coRdon documentation built on Nov. 8, 2020, 5:28 p.m.