Create a dotplot for functional enrichment analysis

This function produces a dotplot to show the results of functional enrichment analyses carried out through over-representation analysis (ORA), gene set enrichment analysis (GSEA), and competitive gene set test accounting for inter-gene correlation (CAMERA). In particular, this function can take as input enrichment results generated by the enrichGenes() function.

Usage

enrichmentDotplot(
  enrichment,
  showTerms = 10,
  showTermsParam = "ratio",
  splitDir = TRUE,
  title = NULL
)

Arguments

enrichment

An object of class FunctionalEnrichment containing enrichment results

showTerms

It is the number of terms to be shown, based on the order determined by the parameter showTermsParam; or, alternatively, a character vector indicating the terms to plot. Default is 10

showTermsParam

The order in which the top terms are selected as specified by the showTerms parameter. It must be one of ratio (default), padj, pval and overlap

splitDir

Logical, if TRUE the resulting plot will be divided in two columns on the basis of enrichment direction (Up and Down). Default is TRUE. This only applies if enrichment method is GSEA or CAMERA

title

The title of the plot. Default is NULL not to include a plot title

Value

A ggplot graph with a dotplot of enrichment results.

Details

When producing a dotplot with this function, significant pathways are ordered on the x-axis on the basis of the ratio between the number of overlapping genes in that set, and the total number of genes in the set. Moreover, the size of each dot is proportional to the number of overlapping features. Finally, the color scale of dots is relative to the adjusted p-values of each category.

Author

Jacopo Ronchi, jacopo.ronchi@unimib.it

Examples

# load example FunctionalEnrichment object
obj <- loadExamples("FunctionalEnrichment")

# plot results
enrichmentDotplot(obj)