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Show Variants by Impacted Columns

Source: R/upsetVarByCol.R
upsetVarByCol.Rd

Produce an UpSet plot showing unique values from a given column

Usage

upsetVarByCol(
  gr,
  var,
  alt_col = "ALT",
  mcol = "transcript_id",
  ...,
  fill = NULL,
  fill_scale = scale_fill_discrete(),
  expand_sets = 0.2,
  hj_sets = 1.1,
  expand_intersect = 0.1,
  vj_intersect = -0.5,
  label_size = 3.5,
  title
)

Arguments

gr

GRanges object with ranges representing a key feature such as exons

var

GRanges object with variants in a given column

alt_col

Column within var containing the alternate allele

mcol

The column within gr to summarise results by

...

Passed to SimpleUpset::simpleUpSet

fill

Optional column in gr used to fill intersections and sets

fill_scale

Discrete ggplot2 scale for filling bars. Ignored if fill = NULL

expand_sets

Expand the set-size x-axis by this amount

hj_sets

Horizontal adjustment of set size labels

expand_intersect

Expand the intersection y-axis by this amount

vj_intersect

Vertical adjustment of intersection size labels

label_size

Control the size of both intersection and sit size labels

title

Summary title to show above the intersection panel. Can be hidden by setting to NULL

Value

An UpSet plot

Details

Take a set of variants, classify them as SNV, Insertion and Deletion, then using a GRanges object, produce an UpSet plot showing impacted values from a given column

See also

SimpleUpset::simpleUpSet

Examples

library(rtracklayer)
library(VariantAnnotation)
library(ggplot2)
gtf <- import.gff(
    system.file("extdata/gencode.v44.subset.gtf.gz", package = "transmogR"),
    feature.type = "exon"
)
vcf <- system.file("extdata/1000GP_subset.vcf.gz", package = "transmogR")
var <- rowRanges(readVcf(vcf, param = ScanVcfParam(fixed = "ALT")))
upsetVarByCol(gtf, var)

upsetVarByCol(
  gtf, var, fill = "transcript_type",
  fill_scale = scale_fill_brewer(palette = "Set1")
)