Plot the PS or DS distribution of a selected set of genes

Source: R/PlotSelectedAgeDistr.R

This function visualizes the PS or DS distribution of a selected set of genes as histogram.

PlotSelectedAgeDistr(
  ExpressionSet,
  gene.set,
  legendName = NULL,
  as.ratio = FALSE,
  use.only.map = FALSE,
  col = "turquoise4",
  xlab = NULL,
  ylab = NULL
)

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.

legendName

a character string specifying whether "PS" or "DS" are are visualized.

as.ratio

logical value indicating whether or not relative frequencies shall be visualized.

use.only.map

logical value indicating whether or not a Phylostratigraphic Map or Divergence Map should be passed to the ExpressionSet argument instead of a standard ExpressionSet object.

col

colour of the bars.

xlab

label of the x-axis.

ylab

label of the y-axis.

See also

PlotDistribution

Author

Hajk-Georg Drost

Examples

data(PhyloExpressionSetExample)

# generate an example gene set
set.seed(123)
ExGeneSet <- sample(PhyloExpressionSetExample[ , 2], 5000)

# gene count example
PlotSelectedAgeDistr(ExpressionSet = PhyloExpressionSetExample,
                     gene.set      = ExGeneSet,
                     legendName    = "PS",
                     as.ratio      = TRUE)


# relative gene count example
PlotSelectedAgeDistr(ExpressionSet = PhyloExpressionSetExample,
                     gene.set      = ExGeneSet,
                     legendName    = "PS",
                     as.ratio      = FALSE)