Plot the results of enrichSEMs

Generates a circular dendrogram, clustering SNP Effect Matrices on similarity and a heatmap representing the -log10 transformed adjusted p-value of a SEMplR enrichment.

Usage

plotEnrich(
  e,
  sem,
  label = "transcription_factor",
  method = "WPCC",
  threshold = 0.05,
  textCols = c("darkgrey", "black"),
  textCex = 0.7,
  heatmapCols = c("white", "red"),
  pvalRange = c(0, 20)
)

Arguments

e

The resulting data.table from enrichSEMs

sem

A SNPEffectMatrixCollection object

label

Column in semData(sem) to use for tree labels

method

Method to use for SEM comparison. See ?universalmotif::compare_motifs for options.

threshold

The adjusted p-value threshold for coloring SEMs

textCols

A vector of two colors to label non-significant and significant SEMs respectively.

textCex

Text size of SEM labels.

heatmapCols

A vector of two colors to use for the heatmap, ordered low to high -log10(padj).

pvalRange

A vector of 2 numerics to use as the scale range for the heatmap of -log10(padj).

Value

a ggtree object

Examples

# load SEMs
data(SEMC)

# note that this is a small example for demonstration purposes
# in actual enrichment analyses sets of 100+ ranges are recommended

# create a GRanges object
gr <- GenomicRanges::GRanges(
    seqnames = "chr12",
    ranges = 94136009
)

# calculate binding propensity
sb <- scoreBinding(gr, SEMC, BSgenome.Hsapiens.UCSC.hg19::Hsapiens)

e <- enrichSEMs(sb, SEMC)
#> Building background set (this may take several minutes) ...
plotEnrich(e, SEMC)