plotSequence {methylscaper} | R Documentation

## Generate Sequence Plot

### Description

Generates an ordered sequence plot of methylation data.

### Usage

    plotSequence(
      orderObject,
      plotFast = TRUE,
      blankWidth = NULL,
      Title = "",
      drawLine = TRUE,
      drawKey = TRUE
    )

### Arguments

`orderObject` | An object of class `orderObject` that contains the processed data and the ordering.
`plotFast` | Logical, setting to FALSE will generate a higher quality plot. TRUE generates a lower resolution file, useful to improve speed while testing. For publication quality use plotFast=TRUE.
`blankWidth` | Indicates the amount of space to leave between the two plots
`Title` | The title of the plot.
`drawLine` | Logical, indicates whether to draw a line above the CG/GC sites.
`drawKey` | Logical, indicates whether to draw a key representing a 147bp nucleosome at the bottom of the plot.

### Value

Output is two side-by-side heatmaps with the endogenous methylation (HCG) on the left and the acciessibility methylation (GCH) on the right. The tick marks at the top indicate either HCG or GCH sites when drawLine=TRUE. If drawKey=TRUE then a black rectangle key is plot at the bottom of the heatmap that is 147 basepairs long. In the HCG plot, red patches represent methylation between two sites; black patches represent unmethylated bases between two unmethylated sites; and gray patches are base pairs which have one methylated site and one unmethylated site flanking. In the HCG plot, yellow patches represent accessibility between two sites; black patches represent occupied bases between two occupied sites; and gray patches are base pairs which have one methylated site and one unmethylated site flanking.

### Examples

    data(singlemolecule_example)

    orderObj <- initialOrder(singlemolecule_example, Method = "PCA")
    plotSequence(orderObj)

[Package methylscaper version 1.2.0 Index]