CoNI (version 0.1.0)

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

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

# NOT RUN {
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")
# }