Plot the Phylostratum or Divergence Stratum Contribution to the Global Pattern

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Description

This function computes the cumulative contribution of each Phylostratum or Divergence Stratum to the global TAI or TDI profile.

Usage

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PlotContribution(ExpressionSet, colors = NULL, legendName = NULL,
  digits.ylab = 3, y.ticks = 5, ...)

Arguments

ExpressionSet

a standard PhyloExpressionSet or DivergenceExpressionSet object.

colors

a character vector specifying the colors that should be used for each Phylostratum/Divergence Stratum. Default: colors = NULL, meaning that default colors are used.

legendName

a character string specifying whether "PS" or "DS" are used to compute relative expression profiles.

digits.ylab

a numeric value specifying the number of digits shown for the TAI or TDI values on the y-axis.

y.ticks

a numeric value specifying the number of ticks to be drawn on the y-axis.

...

additional plot parameters.

Details

Introduced by Domazet-Loso and Tautz (2010), this function allows users to visualize the cumulative contribution of each Phylostratum or Divergence Stratum to the global Transcriptome Age Index or Transcriptome Divergence Index profile to quantify how each Phylostratum or Divergence Stratum influences the profile of the global TAI or TDI pattern.

Author(s)

Hajk-Georg Drost

References

Domazet-Loso T. and Tautz D. (2010). A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature (468): 815-818.

See Also

pTAI, pTDI, TAI, TDI, PlotPattern

Examples

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 data(PhyloExpressionSetExample)
 data(DivergenceExpressionSetExample)
 
 # visualize phylostratum contribution to global TAI
 PlotContribution(PhyloExpressionSetExample, legendName = "PS")
 
 # visualize divergence stratum contribution to global TDI
 PlotContribution(DivergenceExpressionSetExample, legendName = "DS")
 

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