CoNI (version 0.1.0)

getstackedGlobalBarplot_and_Grid: Stacked Global Barplot Side-by-side (two treatments)

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. Results of both Treatments are side by side for better comparison.

Usage

getstackedGlobalBarplot_and_Grid(
  CompTreatTable,
  Treat1,
  Treat2,
  ggrep = TRUE,
  max_pairsLegend = 1,
  force = 0.1,
  mx.overlaps = Inf,
  szggrepel = 6,
  xlb = "Vertex-Class Pairs",
  ...
)

Arguments

CompTreatTable

Output of Compare_VertexClasses_sharedEdgeFeatures

Treat1

Name treatment 1 as in table CompTreatTable

Treat2

Name treatment 2 as in table CompTreatTable

ggrep

logical. If TRUE includes ggrepel labels for every bar

max_pairsLegend

If number of Edge Features >= max_pairsLegend, display number of Edge Features as ggrepel label

force

Repelling force for ggrepel labels

mx.overlaps

Max number of overlaps ggrepel

szggrepel

Size ggrepel labels

xlb

Name for x-axis

...

Other parameters for inner functions, mainly ggplot2 visual parameters

Value

A gtable containing stacked barplots. The barplots show the vertex-class pairs profile of all shared edge features between two treatments (one bar plot per treatment). Every bar consists of multiple edge features that are depicted with different colors

Examples

# NOT RUN {
data(VertexClassesSharedGenes_HFDvsChow)
VCSGs<-VertexClassesSharedGenes_HFDvsChow
HFD_vs_Chow_stackedBarplot<-getstackedGlobalBarplot_and_Grid(VCSGs,
                                                             Treat1 = "HFD",
                                                             Treat2 = "Chow",
                                                             xlb = "Metabolite-class-pairs",
                                                             max_pairsLegend=9)
plot(HFD_vs_Chow_stackedBarplot)
# }