plot_feature_tbl: Staggered plot of genes in interval

In byandell/CCSanger: Utilities to get and use Sanger data for Collaborative Cross

Description

Plot genes as rectangles followed by names. Stagger genes for easy reading. Written original by Dan Gatti 2013-02-13

Usage

plot_feature_tbl(x, rect_col = "grey70", strand_col = c(`-` = "#1b9e77", `+`
  = "#d95f02"), type_col = c(gene = "black", pseudogene = "#1b9e77", other =
  "#d95f02"), text_size = 3, xlim = NULL, snp_pos = top_snps_tbl$pos,
  snp_lod = top_snps_tbl$lod, top_snps_tbl = NULL, snp_col = "grey70",
  extend = 5000, ...)

## S3 method for class 'feature_tbl'
autoplot(x, ...)

## S3 method for class 'feature_tbl'
plot(x, ...)

Arguments

x	tbl of gene information from query_variants; see package qtl2db
rect_col	fill color of rectangle (default "grey70")
strand_col	edge color of rectangle by strand from x (default -="blue", +="red"; none if NULL)
type_col	color of type from x (default "black" for gene, "blue" for pseudogene; none if NULL)
text_size	size of text (default 3)
xlim	horizontal axis limits (default is range of features)
snp_pos	position of SNPs in bp if used (default NULL)
snp_lod	LOD of SNPs (for color plotting)
top_snps_tbl	table from top_snps
snp_col	color of SNP vertical lines (default "grey70")
extend	extend region for SNPs in bp (default 5000)
...	additional arguments (not used)

Value

data frame of gene information (invisible)

Author(s)

Brian S Yandell, [e-mail] Daniel Gatti, [e-mail]

References

https://github.com/dmgatti/DOQTL/blob/master/R/gene.plot.R

byandell/CCSanger documentation built on May 13, 2019, 9:26 a.m.