Display integrated miRNA-mRNA augmented pathways in a dotplot

This function produces a dotplot that depicts the results of a topologically-aware integrative pathway analysis (TAIPA) carried out through the topologicalAnalysis() function.

Usage

integrationDotplot(
  object,
  showTerms = 10,
  showTermsParam = "normalized.score",
  title = NULL
)

Arguments

object: An object of class IntegrativePathwayAnalysis
showTerms: It is the number of pathways to be shown, based on the order determined by the parameter showTermsParam; or, alternatively, a character vector indicating the pathways to plot. Default is 10
showTermsParam: The order in which the top pathways are selected as specified by the showTerms parameter. It must be one of coverage, padj, pval, score and normalized.score (default)
title: The title of the plot. Default is NULL not to include a plot title

Value

A ggplot graph with a dotplot of integrated pathways.

Details

When producing the dotplot with this function, significant pathways are ordered on the x-axis on the basis of their normalized pathway score computed by topologicalAnalysis(). The higher is this score, and the more affected a pathway is between biological conditions. Moreover, the size of each dot is equal to the ratio between the number of nodes for which a measurement is available, and the total number of nodes (pathway coverage). Finally, the color scale of dots is relative to the adjusted p-values of each pathway.

Author

Jacopo Ronchi, jacopo.ronchi@unimib.it

Examples

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

# create a dotplot of integrated pathways
integrationDotplot(obj)