plotDot: Generate dot plot from Anchor files
In maize-genetics/rPHG: R front-end for the practical haplotype graph

plotDot

R Documentation

Generate dot plot from Anchor files

Description

This function will generate a dot plot (collinearity) from an Anchor File generated from the program [AnchorWave](https://github.com/baoxingsong/AnchorWave). This is one of the preliminary steps in creating a PHG database.

Usage

plotDot(
  anchorPath,
  querySeqId = NULL,
  refSeqId = NULL,
  queryLab = NULL,
  refLab = NULL,
  colorId = c("strand", "score")
)

Arguments

`anchorPath`	Path to anchor file.
`querySeqId`	Vector of sequence IDs (query).
`refSeqId`	Vector of sequence IDs (reference).
`queryLab`	Optional label for query axis.
`refLab`	Optional label for reference axis.
`colorId`	How to color plots (`strand` or `score`)