shift: Shift bins left/right

In thackl/gggenomes: A Grammar of Graphics for Comparative Genomics

Shift bins left/right

Description

Shift bins along the x-axis, i.e. left or right in the default plot layout. This is useful to align feats of interest in different bins.

Usage

shift(x, bins = everything(), by = 0, center = FALSE)

Arguments

x	gggenomes object
bins	to shift left/right, select-like expression
by	shift each bin by this many bases. Single value or vector of the same length as bins.
center	horizontal centering

Value

gggenomes object with shifted seqs

Examples

p0 <- gggenomes(emale_genes, emale_seqs) +
  geom_seq() + geom_gene()

# Slide one bin left and one bin right
p1 <- p0 |> shift(2:3, by = c(-8000, 10000))

# align all bins to a target gene
mcp <- emale_genes |>
  dplyr::filter(name == "MCP") |>
  dplyr::group_by(seq_id) |>
  dplyr::slice_head(n = 1) # some have fragmented MCP gene, keep only first

p2 <- p0 |> shift(all_of(mcp$seq_id), by = -mcp$start) +
  geom_gene(data = genes(name == "MCP"), fill = "#01b9af")

library(patchwork)
p0 + p1 + p2

thackl/gggenomes documentation built on Aug. 31, 2024, 9:47 p.m.