ggtmap: Make a transcriptome map using the ggplot2 framework.

In churchill-lab/qtl2tricks: Tricks for Karl Broman's qtl2.

Description

Make a transcriptome map using the ggplot2 framework.

Usage

ggtmap(data, color.points = FALSE, cis.points = FALSE,
  cis.radius = 2, cis.color = "#4286f4")

Arguments

data:

data.frame (or tibble) with the following columns: ensembl: (required) character string containing the Ensembl gene ID. qtl_chr: (required) character string containing QTL chromsome. qtl_pos: (required) floating point number containing the QTL position in Mb. qtl_lod: (optional) floating point number containing the LOD score. gene_chr: (optional) character string containing transcript chromosome. gene_start: (optional) character string containing transcript start postion in Mb. gene_end: (optional) character string containing transcript end position in Mb. color.points: logical that is TRUE if the points should be colored by LOD. cis.points: logical that is TRUE if the points should be colored if they are with in cis. cis.radius: numeric value containing the radius in Mb between a gene and a cis-eQTL. Optional. cis.color: color for cis QTL. Optional.

Value

plot of the QTL and gene location for each gene.

churchill-lab/qtl2tricks documentation built on May 20, 2019, 1:13 p.m.