create_stackedGlobalBarplot_perTreatment: Stacked Global Barplot (One treatment)

In CoNI: Correlation Guided Network Integration (CoNI)

Description

This function will create a stacked barplot from the output of Compare_VertexClasses_sharedEdgeFeatures using all shared Edge Features (e.g., genes) between two treatments.

Usage

create_stackedGlobalBarplot_perTreatment(
  CompTreatTable,
  treat = NULL,
  xlb = "Vertex-Class Pairs",
  ylb = "Number of pairs",
  max_pairsLegend = 2,
  mx.overlaps = Inf,
  szggrepel = 6,
  force = 0.1,
  szTitle = 12,
  szaxisTxt = 12,
  szaxisTitle = 12,
  ylim = NULL
)

Arguments

CompTreatTable	Output of Compare_VertexClasses_sharedEdgeFeatures
treat	Name of treatment to display. It should match the column name in the output of Compare_VertexClasses_sharedEdgeFeatures
xlb	Name for x-axis
ylb	Name for y-axis
max_pairsLegend	If number of Edge Features >= max_pairsLegend, display number of Edge Features as label with ggrepel
mx.overlaps	Max number of overlaps ggrepel
szggrepel	Size ggrepel labels
force	Repelling force for ggrepel labels
szTitle	Size Title
szaxisTxt	Size axis text
szaxisTitle	Size axis titles
ylim	Optional y-limits of the plot

Value

A ggplot object to create a stacked barplot. The stacked barplot shows the vertex-class pairs profile of all shared edge features but restricted to a single treatment. Every bar consists of multiple edge features (stacked) that are represented with different colors

Examples

data(VertexClassesSharedGenes_HFDvsChow)
create_stackedGlobalBarplot_perTreatment(CompTreatTable = VertexClassesSharedGenes_HFDvsChow,
                                         treat = "HFD",
                                         max_pairsLegend = 9,
                                         xlb = "Metabolite-class-pairs")

CoNI documentation built on Sept. 30, 2021, 5:09 p.m.