plotComb2Samples: Plots the correlation in gene expression between two samples

Description Usage Arguments Author(s) References See Also Examples

View source: R/plotSmoothScat.R

Description

Plots the correlation in gene expression between two samples. Each dot represents a gene, and the dots have a density-dependent coloring. Genes with exceptional behavior can be highlighted by showing their gene symbol.

Usage

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plotComb2Samples(object, x, y, trsholdX = NULL, trsholdY = NULL, probe2gene = TRUE, ...)

Arguments

object

ExpressionSet object for the experiment

x

String containing the name of the first sample. This should be a the name of a column in the exprs data of the expressionSet object.

y

String containing the name of the second sample. See x

trsholdX

Vector of two values specifying the X-axis thresholds within which genes should be highlighted by their gene symbol.

trsholdY

Vector of two values specifying the Y-axis thresholds within which genes should be highlighted by their gene symbol.

probe2gene

Boolean indicating whether the probeset should be translated to a gene symbol (used for the default title of the plot)

...

Possibility to add extra plot options. See par

Author(s)

W. Talloen

References

~put references to the literature/web site here ~

See Also

plotCombMultSamples

Examples

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if (require(ALL)){
  data(ALL, package = "ALL")
  ALL <- addGeneInfo(ALL)

  plotComb2Samples(ALL,"84004", "01003",
    trsholdX = c(10,12), trsholdY = c(4,6),
	xlab = "a B-cell", ylab = "a T-cell")
}

a4Base documentation built on Nov. 1, 2018, 2:40 a.m.