Plot the Mean Expression Profiles of Phylostrata or Divergence Strata

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Description

This function computes for each phylostratum or divergence-stratum the corresponding mean expression profile and plots the profiles in N different windows corresponding to the given Phylostratum-Classes that shall be compared.

Usage

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PlotMeans(ExpressionSet, Groups = NULL, legendName = NULL, colors = NULL,
  ...)

Arguments

ExpressionSet

a standard PhyloExpressionSet or DivergenceExpressionSet object.

Groups

a list containing the phylostrata or divergence-strata that correspond to the same phylostratum class or divergence class. For ex. evolutionary old phylostrata: PS1-3 (Class 1) and evolutionary young phylostrata: PS4-12 (Class 2). In this case, the list could be assigned as, Groups = list(c(1:3), c(4:12)). It is also possible to define more than 2 groups of evolutionary ages. For ex. Groups = list(c(1:3),c(4:8),c(9:12)).

legendName

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

colors

colors for mean expression profiles. Default: colors = NULL, hence default colours are used.

...

default graphics parameters.

Details

This plot may be useful to compare the absolute mean expression levels of each phylostratum or divergence-stratum class.

In different developmental processes different phylostratum or divergence-stratum classes might be more expressed than others, hence contributing more to the overall phylotranscriptomics pattern (TAI or TDI). This plot can help to identify the phylostratum or divergence-stratum classes that contributes most to the overall transcriptome of the given developmental process.

Value

a plot showing mean expression profiles of phylostrata or divergence-strata corresponding to the same phylostratum class or divergence class.

Author(s)

Hajk-Georg Drost

See Also

PlotBarRE, RE, REMatrix, PlotRE

Examples

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# load PhyloExpressionSet
data(PhyloExpressionSetExample)

# load PhyloExpressionSet
data(DivergenceExpressionSetExample)

# plot evolutionary old PS (PS1-3) vs evolutionary young PS (PS4-12)
PlotMeans(PhyloExpressionSetExample,Groups = list(c(1:3), c(4:12)), 
          legendName = "PS", lty = 1, lwd = 5)

# plot conserved DS (DS1-5) vs divergent DS (PS6-10)
# NOTE: DS are always defined in the range 1, 2, ... , 10.
# Hence, make sure that your groups are within this range!
PlotMeans(DivergenceExpressionSetExample,Groups = list(c(1:5), c(6:10)), 
          legendName = "DS", lty = 1, lwd = 5)


# adding custom colors for relative expression levels:
# -> colors should be ordered by PS/DS starting with PS1,2,3...
PlotMeans(PhyloExpressionSetExample,
       Groups     = list(c(1:3), c(4:12)), 
       legendName = "PS",
       colors     = c("black","red","green","brown","darkmagenta",
       "blue","darkred","darkblue","darkgreen", "orange",
       "azure4","gold4"), 
       lty        = 1, 
       lwd        = 5)

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