position_variant: Plot types of mutations with different offsets

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

Plot types of mutations with different offsets

Description

position_variant() allows the user to plot the different mutation types (e.g. del, ins, snps) at different offsets from the base. This can especially be useful to highlight in which regions certain types of mutations have higher prevalence. This position adjustment is most relevant for the analysis/visualization of VCF files with the function geom_variant().

Usage

position_variant(offset = c(del = 0.1, snp = 0, ins = -0.1), base = 0)

Arguments

offset	Shifts the data up/down based on the type of mutation. By default offset = c(del=0.1, snp=0, ins=-0.1). The user can supply an own vector to offset to indicate at which offsets the different mutation types should be plotted. Types of mutations that have not been specified within the vector, will be plotted with an offset of 0.
base	How to align the offsets relative to the sequence. At base = 0, plotting of the offsets starts from the sequence. base thus moves the entire feature up/down.

Examples

# Creation of example data. 
testposition <- tibble::tibble(
type = c("ins", "snp", "snp", "del", "del", "snp", "snp", "ins", "snp", "ins", "snp"),
start = c(10, 20, 30, 35, 40, 60, 65, 90, 90, 100, 120),
end = start + 1,
seq_id = c(rep("A", 11)))
testseq <- tibble::tibble(
seq_id = "A",
start = 0,
end = 150,
length = end-start)

p <- gggenomes(seqs = testseq, feats = testposition)

#This first plot shows what is being plotted when only geom_variant is called
p + geom_variant()

#Next lets use position_variant, and change the shape aesthetic by column `type`
p + geom_variant(aes(shape = type), position = position_variant()) 

#Now lets create a plot with different offsets by inserting a self-created vector.
p + geom_variant(
  aes(shape = type),
  position = position_variant(c(del=0.4, ins =-0.4))
) + scale_shape_variant()

#Changing the base will shift all points up/down relatively from the sequence.
p + geom_variant(
  aes(shape = type),
  position=position_variant(base = 0.5)
) + geom_seq()

thackl/gggenomes documentation built on March 10, 2024, 7:26 a.m.