Sequence logo annotation — annoSeqlogo • monaLisa

create an annotation for a Heatmap containing sequence logos.

annoSeqlogo(
  grobL,
  which = c("column", "row"),
  space = unit(0.5, "mm"),
  width = NULL,
  height = NULL,
  gp = gpar(fill = NA, col = NA)
)

Arguments

grobL: A list of sequence logo grobs, typically created using seqLogoGrob.
which: Whether it is a column annotation or a row annotation?
space: The space around the image to the annotation grid borders. The value should be a unit object.
width: Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.
height: Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.
gp: Graphic parameters for annotation grids. Can be used to control the background color in the annotation grids.

Value

An annotation function which can be used in

HeatmapAnnotation.

Examples

if (require(JASPAR2020) && require(TFBSTools) && require(gridExtra)) {
    pfm1 <- getMatrixByID(JASPAR2020, "MA0139")

    g1 <- seqLogoGrob(pfm1)

    anno <- annoSeqlogo(list(g1))
}
#> Loading required package: JASPAR2020
#> Loading required package: TFBSTools
#> Loading required package: gridExtra