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

Description Usage Arguments Value Examples

View source: R/epiGPlotFunctions.R

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

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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

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## 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.