Plot non-alt versus alt binding propensity for a single variant — plotSEMMotifs • SEMplR

Plot non-alt versus alt binding propensity for a single variant

Usage

plotSEMMotifs(
  s,
  variant,
  label = "transcription_factor",
  labsize = 4,
  cols = c("#F8766D", "dodgerblue2"),
  ptsize = 1
)

Arguments

s: a SEMplScores object with scores populated
variant: variant id to plot
label: column in sem_metadata slot of semplObj to use for point labels
labsize: numeric size of the point labels
cols: vector of length 2 with colors to use for plotting gained and lost motifs respectively
ptsize: numeric size of the ggplot points

Value

a ggplot scatter plot of non-alt binding propensity versus alt binding propensity

Examples

library(VariantAnnotation)
data(SEMC)

# create a VRanges object
vr <- VRanges(
    seqnames = "chr12",
    ranges = 94136009,
    ref = "G", alt = "C"
)

# calculate binding propensity
s <- scoreVariants(vr, SEMC, BSgenome.Hsapiens.UCSC.hg19::Hsapiens)

plotSEMMotifs(s, "chr12:94136009:G>C", label = "transcription_factor")