PlotGeneSet: Plot the Expression Profiles of a Gene Set

In YTLogos/myTAI: Evolutionary Transcriptomics

Description

This function simply visualizes the gene expression profiles of a defined subset of genes stored in the input ExpressionSet.

Usage

PlotGeneSet(ExpressionSet, gene.set, get.subset = FALSE,
  use.only.map = FALSE, colors = NULL, plot.legend = TRUE, y.ticks = 6,
  digits.ylab = 4, ...)

Arguments

ExpressionSet	a standard PhyloExpressionSet or DivergenceExpressionSet object.
gene.set	a character vector storing the gene ids for which gene expression profiles shall be visualized.
get.subset	a logical value indicating whether or not an ExpressionSet subset of the selected gene.set should be retuned.
use.only.map	a logical value indicating whether instead of a standard ExpressionSet only a Phylostratigraphic Map or Divergene Map is passed to the function.
colors	colors for gene expression profiles. Default: colors = NULL, hence default colours are used.
plot.legend	a logical value indicating whether gene ids should be printed as legend next to the plot.
y.ticks	a numeric value specifying the number of ticks to be drawn on the y-axis.
digits.ylab	a numeric value specifying the number of digits shown for the expression levels on the y-axis.
...	additional parameters passed to matplot.

Details

This function simply visualizes or subsets the gene expression levels of a set of genes that are stored in the input ExpressionSet.

Author(s)

Hajk-Georg Drost

See Also

SelectGeneSet, PlotEnrichment, DiffGenes

Examples

data(PhyloExpressionSetExample)

# the best parameter setting to visualize this plot:
# png("test_png.png",700,400)
PlotGeneSet(ExpressionSet = PhyloExpressionSetExample, 
            gene.set      = PhyloExpressionSetExample[1:5, 2], 
            type          = "l", 
            lty           = 1, 
            lwd           = 4,
            xlab          = "Ontogeny",
            ylab          = "Expression Level")

# dev.off()

# In case you would like to work with the expression levels
# of selected genes you can specify the 'get.subset' argument:

PlotGeneSet(ExpressionSet = PhyloExpressionSetExample, 
            gene.set      = PhyloExpressionSetExample[1:5, 2], 
            get.subset    = TRUE)


# get a gene subset using only a phylostratihraphic map
ExamplePSMap <- PhyloExpressionSetExample[ , 1:2]

PlotGeneSet(ExpressionSet = ExamplePSMap, 
            gene.set      = PhyloExpressionSetExample[1:5, 2], 
            get.subset    = TRUE,
            use.only.map  = TRUE)
            

YTLogos/myTAI documentation built on May 19, 2019, 1:46 a.m.