geom_motif {motifStack} | R Documentation

## geom_motif

### 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)

[Package motifStack version 1.31.2 Index]