scatterPlot: scatterPlot Plot GO terms as scattered points.

In imbforge/rrvgo: Reduce + Visualize GO

scatterPlot Plot GO terms as scattered points.

Description

scatterPlot Plot GO terms as scattered points.

Usage

scatterPlot(
  simMatrix,
  reducedTerms,
  algorithm = c("pca", "umap"),
  onlyParents = FALSE,
  size = "score",
  addLabel = TRUE,
  labelSize = 3
)

Arguments

simMatrix	a (square) similarity matrix.
reducedTerms	a data.frame with the reduced terms from reduceSimMatrix()
algorithm	algorithm for dimensionality reduction. Either pca or umap.
onlyParents	plot only parent terms. Point size is the number of aggregated terms under the parent.
size	what to use as point size. Can be either GO term's "size" or "score".
addLabel	add labels with the most representative term of the group.
labelSize	text size in the label.

Details

Distances between points represent the similarity between terms. Axes are the first 2 components of applying one of this dimensionality reduction algorithms: - a PCoA to the (di)similarity matrix. - a UMAP (Uniform Manifold Approximation and Projection,[1]) Size of the point represents the provided scores or, in its absence, the number of genes the GO term contains.

Value

ggplot2 object ready to be printed (or manipulated)

References

[1] Konopka T (2022). _umap: Uniform Manifold Approximation and Projection_. R package version 0.2.8.0, https://CRAN.R-project.org/package=umap.

Examples

go_analysis <- read.delim(system.file("extdata/example.txt", package="rrvgo"))
simMatrix <- calculateSimMatrix(go_analysis$ID, orgdb="org.Hs.eg.db", ont="BP", method="Rel")
scores <- setNames(-log10(go_analysis$qvalue), go_analysis$ID)
reducedTerms <- reduceSimMatrix(simMatrix, scores, threshold=0.7, orgdb="org.Hs.eg.db")
scatterPlot(simMatrix, reducedTerms)

imbforge/rrvgo documentation built on March 15, 2024, 4:40 a.m.