Description Usage Arguments Value Examples
View source: R/epiGPlotFunctions.R
Plots the expression vs quantile data in a scatterplot, linear regression can be visualized for user-specified sample class amongst other user-specified parameters
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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 |
Returns a plot that user can assign from its return value.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## 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)
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