PlotRE: Plot Relative Expression Levels

Description Usage Arguments Details Value Author(s) References See Also Examples

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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