plotSequence: Generate Sequence Plot

In rhondabacher/methylscaper: Visualization of Methylation Data

Generate Sequence Plot

Description

Generates an ordered sequence plot of methylation data.

Usage

plotSequence(
  orderObject,
  plotFast = TRUE,
  blankWidth = NULL,
  Title = "",
  drawLine = TRUE,
  drawKey = TRUE,
  shinySizer = 0
)

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.
shinySizer	internal sizing parameter for plot layout in shiny app.

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)

rhondabacher/methylscaper documentation built on Oct. 10, 2024, 8:18 a.m.