summary.feature_tbl {qtl2pattern}

Summary of features

Description

Show count min and max of features by type

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

Usage

## S3 method for class 'feature_tbl'
summary(object, major = TRUE, ...)

## S3 method for class 'feature_tbl'
subset(x, start_val = 0, stop_val = max(x$stop), ...)

ggplot_feature_tbl(
  object,
  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 = 0.005,
  ...
)

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

Arguments

object

tbl of gene information from query_variants; see create_variant_query_func

major

if TRUE (default), only summarize genes and exons

...

additional arguments (not used)

x

tbl of feature information from get_feature_snp

start_val, stop_val

start and stop positions for subset

rect_col

fill color of rectangle (default "grey70")

strand_col

edge color of rectangle by strand from object (default -="blue", +="red"; none if NULL)

type_col

color of type from object (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 0.005)

Value

tbl of feature summaries by type

tbl of feature summaries by type

data frame of gene information (invisible)

Author(s)

Brian S Yandell, [e-mail]

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

References

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