Plot Relative Expression Levels

Description

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

For each phylostratum or divergence-stratum the corresponding relative expression profile is being computed as follows:

f_js = ( e_js - e_j min ) / ( e_j max - e_j min )

where e_j min and e_j max denote the minimum/maximum mean expression level of phylostratum j over developmental stages s. This linear transformation corresponds to a shift by e_j min and a subsequent shrinkage by e_j max - e_j min. As a result, the relative expression level f_js of developmental stage s with minimum e_js is 0, the relative expression level f_js of the developmental stage s with maximum e_js is 1, and the relative expression levels f_js of all other stages s range between 0 and 1, accordingly.

Usage

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PlotRE(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.

legendName

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

colors

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

...

default graphics parameters.

Details

Studying the relative expression profiles of each phylostratum or divergence-stratum enables the detection of common gene expression patterns shared by several phylostrata or divergence-strata.

Finding similar relative expression profiles among phylostrata or divergence-strata suggests that phylostrata or divergence-strata sharing a similar relative expression profile are regulated by similar gene regulatory elements. Hence, these common phylostrata or divergence-strata might govern similar processes in the given developmental time course.

Value

a plot showing the relative expression profiles of phylostrata or divergence-strata belonging to the same group.

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.

Quint M et al. 2012. "A transcriptomic hourglass in plant embryogenesis". Nature (490): 98-101.

See Also

PlotBarRE, RE, REMatrix

Examples

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# read standard phylotranscriptomics data
data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)

# example PhyloExpressionSet
PlotRE(PhyloExpressionSetExample,Groups = list(c(1:3), c(4:12)), 
       legendName = "PS", lty = 1, lwd = 5)


# or you can choose any combination of groups
PlotRE(PhyloExpressionSetExample,Groups = list(c(1,7,9), c(2:6,8,10:12)),
       legendName = "PS", lty = 1, lwd = 5)

# or multiple groups
PlotRE(PhyloExpressionSetExample,Groups = list(c(1,7,9), c(3:6,8),c(2,10:12)),
       legendName = "PS", lty = 1, lwd = 5)
       
       
       
# example DivergenceExpressionSet
PlotRE(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...
PlotRE(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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