plotNeighborsOrientation: Stacked barplot of gene orientations for upstream and...

In pgpmartin/GeneNeighborhood: Analyze the Neighborhood (Upstream/Downstream Neighbors) of Genes

Description

Plots stacked bars of the percentage of each orientation for the upstream and downstream genes.

Usage

plotNeighborsOrientation(orientationStats)

Arguments

orientationStats

A data frame produced by the analyzeNeighborsOrientation function

Details

The function only plots the following orientations, if present:

• SameStrand. The upstream/downstream gene is on the same strand as the focus gene

• OppositeStrand. The upstream/downstream gene is on the opposite strand of the focus gene

• OppositeOverlap. The upstream/downstream gene is on the opposite strand of the focus gene and overlaps with the focus gene

• SameOverlap. The upstream/downstream gene is on the same strand of the focus gene and overlaps with the focus gene

• other. Any other, more complex situation (e.g. multiple overlaps, focus gene contained within another gene, etc.)

Value

A ggplot object

Author(s)

Pascal GP Martin

See Also

ggplot2, ggplot

Examples

## Obtain gene neighborhood information:
  GeneNeighbors <- getGeneNeighborhood(Genegr)
## Define a (random) set of (100) genes:
  set.seed(123)
  randGenes <- sample(names(Genegr), 100)
## Analyze the orientation of their neighbors:
  NOS <- analyzeNeighborsOrientation(randGenes, GeneNeighborhood = GeneNeighbors)
## Plot the results:
  plotNeighborsOrientation(NOS)

pgpmartin/GeneNeighborhood documentation built on Sept. 2, 2021, 6:37 a.m.