Plot non-alt versus alt binding propensity for a single motif — plotSEMVariants • SEMplR

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

Usage

plotSEMVariants(
  s,
  sem,
  label = "varId",
  labsize = 4,
  cols = c("#F8766D", "dodgerblue2"),
  ptsize = 1
)

Arguments

s: a SEMplScores object with scores populated
sem: a single character vector matching a semId in the semplObj
label: column in scores 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)

plotSEMVariants(s, "IKZF1_HUMAN.GM12878")