geom_motif: geom_motif

In motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

Description

geom_motif uses the locations of the four corners (xmin, xmax, ymin and ymax) to plot motifs.

Usage

geom_motif(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  ic.scale = TRUE,
  use.xy = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

mapping	Set of aesthetic mappings created by aes() or aes_(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.
data	The data to be displayed in this layer.
stat	The statistical transformation to use on the data for this layer, as a string.
position	Position adjustment, either as a string, or the result of a call to a position adjustment function.
...	Other arguments passed on to layer().
ic.scale	logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.
use.xy	logical If TRUE, the required aesthethics will be x, y, width, height, and motif. Otherwise, xmin, ymin, xmax, ymax and motif.
show.legend	Not used.
inherit.aes	If FALSE, overrides the default aesthetics, rather than combining with them.

Value

a layer that contains GeomMotif object.

Aesthetics

geom_motif() understands the following aesthetics (required aesthetics are in bold):

• xmin

• xmax

• ymin

• ymax

• motif

• angle

• fontfamily

• fontface

OR

• x

• y

• width

• height

• motif

• angle

• fontfamily

• fontface

Author(s)

Jianhong Ou

Examples

pcm <- read.table(file.path(find.package("motifStack"), 
                            "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA")

df <- data.frame(xmin=c(.25, .25), ymin=c(.25, .75), xmax=c(.75, .75), ymax=c(.5, 1))
df$motif <- list(pcm2pfm(motif), pcm2pfm(motif))

library(ggplot2)
ggplot(df, aes(xmin=xmin, ymin=ymin, xmax=xmax, ymax=ymax, motif=motif)) + 
geom_motif() + theme_bw() + ylim(0, 1) + xlim(0, 1)

motifStack documentation built on Nov. 8, 2020, 7:43 p.m.