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

In drostlab/myTAI: Evolutionary Transcriptomics

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

Description

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

Usage

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.

Author(s)

Hajk-Georg Drost

See Also

PlotDistribution

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)

drostlab/myTAI documentation built on April 8, 2024, 8:24 a.m.