getVertexsPerEdgeFeature: Vertex Class profile per edge feature (one treatment)

In CoNI: Correlation Guided Network Integration (CoNI)

Description

This function creates a barplot or barplots showing the number of vertex features per class for every shared edge feature between two treatments

Usage

getVertexsPerEdgeFeature(
  CompTreatTable,
  Annotation,
  chunks = 5,
  treat = NULL,
  small = FALSE,
  ggrep = TRUE,
  xlb = "Gene",
  onlyTable = FALSE,
  szTitle = 12,
  szaxisTxt = 12,
  szaxisTitle = 12,
  ...
)

Arguments

CompTreatTable	Output of Compare_VertexClasses_sharedEdgeFeatures
Annotation	Data frame that includes the rgb colors for every class. The column 'class' (or 'Class') has to be present and also the column 'ColorRgb'
chunks	To avoid a non readable dense plot the results can be spitted in multiple plots
treat	Specify the treatment for which the plot will be created. It should be one of the two treatments in the output of Compare_VertexClasses_sharedEdgeFeatures
small	logical. If only a few edge features are in the input set as TRUE. A single plot will be created
ggrep	logical. If TRUE includes ggrepel labels for every bar
xlb	x-axis label
onlyTable	logical. If TRUE a table is returned instead of a plot
szTitle	Size title
szaxisTxt	Size axis text
szaxisTitle	Size axis title
...	Other parameters for inner functions, mainly ggplot2 visual parameters

Value

A list of ggplot objects to create different barplots. The barplots show the number of vertex features per class for every shared edge feature between two treatments. The barplots restrict to one of the compared treatments. An alternative output is a data.frame with the number of vertex features per class and edge feature (onlyTable=TRUE)

Examples

data(VertexClassesSharedGenes_HFDvsChow)
data(MetColorTable)
#Note: No differences in example as all the Output of CoNI was kept
getVertexsPerEdgeFeature(CompTreatTable = VertexClassesSharedGenes_HFDvsChow,
                         Annotation = MetColorTable,
                         chunks = 2,
                         treat = "HFD")

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