scatterPlot {rrvgo} | R Documentation

## scatterPlot Plot GO terms as scattered points.

### Description

scatterPlot Plot GO terms as scattered points.

### Usage

    scatterPlot(
      simMatrix,
      reducedTerms,
      size = "score",
      addLabel = TRUE,
      labelSize = 3
    )

### Arguments

`simMatrix` | a (square) similarity matrix.
`reducedTerms` | a data.frame with the reduced terms from reduceSimMatrix()
`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 a PCoA to the (di)similarity matrix. Size of the point represents the provided scores or, in its absence, the number of genes the GO term contains.

### Value

ggplot2 object raedy to be printed (or manipulated)

### 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)

[Package rrvgo version 1.4.4 Index]