plotEpigeneticEV: Plots the the expression values of a epigenetic gene.

In kevbobli224/EpiGPlot: Visualization of epigenetic factors

Description

Plots the expression vs quantile data in a scatterplot, linear regression can be visualized for user-specified sample class amongst other user-specified parameters

Usage

plotEpigeneticEV(
  layout,
  normalized = FALSE,
  colour.legend = TRUE,
  colour.grey = FALSE,
  size.arrow = 1,
  size.pred = 1,
  labels.which = NULL,
  labels.top = 0,
  labels.size = 3,
  sample.class = NULL,
  sample.pred = NULL
)

Arguments

layout	An n by 4 data frame containing necessary information of epigenetic genes information, usually loaded by the package's given function; see parseEpigeneticData and loadEpigeneticData
normalized	Whether the dataset "layout" expression value is normalized.
colour.legend	Whether legend on the plot should be dispalyed
colour.grey	Whether if greyscale should be applied to all visual details of the plot
size.arrow	The size of the line segment if user chooses to display top expression values
size.pred	The size of linear regression model's line segment if user chooses to display predictions on sample class
labels.which	User can specify which sample to be displayed on the plot through a list/vector
labels.top	User can specify how many highest expression value samples to be displayed
labels.size	The font size of sample names
sample.class	User can specify which sample class to display
sample.pred	User can specify which sample class to perform linear regression on, and display their respective line segments

Value

Returns a plot that user can assign from its return value.

Examples

## Not run: 
rawData <- EpiGPlot::loadEpigeneticData("data/NO66_HUMAN.rda")
gLayout <- EpiGPlot::layoutEpigeneticEV(rawData,
                                        normalized=TRUE,
                                        sample.class=c("cell_line", "tissue"))
gPlot <- EpiGPlot::plotEpigeneticEV(gLayout,
                                    normalized=TRUE,
                                    sample.pred = c("tissue"),
                                    labels.top=5)
gPlot

gPlot <-
EpiGPlot::plotEpigeneticEV(gLayout, sample.pred = c("tissue", "cell_line"),
                         labels.which=c("chronic lymphocytic leukemia (T-CLL) cell line:SKW-3"))

gPlot

## End(Not run)

kevbobli224/EpiGPlot documentation built on Dec. 21, 2021, 6:35 a.m.