annoSeqlogo: Sequence logo annotation

In fmicompbio/monaLisa: Binned Motif Enrichment Analysis and Visualization

Sequence logo annotation

Description

create an annotation for a Heatmap containing sequence logos.

Usage

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))
}

fmicompbio/monaLisa documentation built on Nov. 2, 2024, 1:33 p.m.