Plot SEM scores for each nucleic acid in each position of the motif

Plot SEM scores for each nucleic acid in each position of the motif

Usage

plotSEM(
  sem,
  motif = NULL,
  motifSeq = NULL,
  cols = c("lightgrey", "dodgerblue"),
  size = 7,
  hindex = NULL,
  hcol = "dodgerblue",
  halpha = 0.1,
  hwidth = 15,
  lcol = "#d7dbdd",
  lwidth = 1
)

Arguments

sem

A SNPEffectMatrix or SNPEffectMatrixCollection object.

motif

sem id to plot. If providing a SNPEffectMatrixCollection object, must match a name in the list. If providing a single SNPEffectMatrix object, this parameter is ignored and the SNPEffectMatrix's semId is used for plotting.

motifSeq

Character sequence to color on plot

cols

A vector of two colors to color the nucleotides not included and included in the provided motifSeq respectively

size

Font size of nucleotides in plot

hindex

Index of nucleotide to highlight in the motifSeq

hcol

The color of the vertical highlight bar

halpha

The alpha transparency of the vertical highlight bar

hwidth

Width of highlight bar

lcol

Color of the horizongtal endogenous and background binding lines

lwidth

Width of the horizontal endogenous and background binding lines

Value

a ggplot with sem scores for each nucleic acid per position

Examples

library(VariantAnnotation)
data(SEMC)

# Given a SNPEffectMatrix Collection
plotSEM(SEMC, motif = "JUN")


# Given a single SNPEffectMatrix
sem <- getSEMs(SEMC, "JUN")
plotSEM(sem)


# color by sequence
plotSEM(sem, motifSeq = "TGAGTCA", hindex = 2)