myTAI (version 0.9.3)

PlotGeneSet: Plot the Expression Profiles of a Gene Set

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.

See Also

SelectGeneSet, PlotEnrichment, DiffGenes

Examples

# NOT RUN {
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)
            
# }