seqLogoGrob: Create a simple sequence logo grob.

In fmicompbio/monaLisa: Binned Motif Enrichment Analysis and Visualization

Create a simple sequence logo grob.

Description

Create a simple sequence logo grob (grid-graphics object) for a transcription factor from a position frequency matrix. The logo drawing code is a simplified version from seqLogo and for example can be used to embedd sequence logos within other plots.

Usage

seqLogoGrob(x, xmax = NULL, ymax = 2, xjust = c("left", "center", "right"))

Arguments

x	A PFMatrix object
xmax	A numeric scalar with the maximal width for the logo (in base-pairs). A value of NULL will scale the logo to the full width of the viewport.
ymax	A numeric scalar with the maximal height for the logo (in bits) A value of NULL will scale the logo to the full height of the viewport.
xjust	A character scalar specifying the horizontal adjustment of the sequence log withint the viewport; one of "left", "center" or "right".

Value

A polygon grob.

See Also

seqLogo for the original, more flexible version of this function.

Examples

if (require(JASPAR2020) && require(TFBSTools) && require(gridExtra)) {
    pfm1 <- getMatrixByID(JASPAR2020, "MA0139")
    pfm2 <- getMatrixByID(JASPAR2020, "MA0531")

    g1 <- seqLogoGrob(pfm1)
    g2 <- seqLogoGrob(pfm2)

    gridExtra::grid.arrange(g1, g2)
}

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