This function computes for each age category the corresponding relative expression profile.
For each age category 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.
PlotRE( ExpressionSet, Groups = NULL, modules = NULL, legendName = "age", xlab = "Ontogeny", ylab = "Relative Expression Level", main = "", y.ticks = 10, adjust.range = TRUE, alpha = 0.008, ... )
a standard PhyloExpressionSet or DivergenceExpressionSet object.
a list containing the age categories for which mean expression levels shall be drawn.
For ex. evolutionary users can compare old phylostrata: PS1-3 (Class 1) and evolutionary young phylostrata: PS4-12 (Class 2).
In this example, the list could be assigned as,
a list storing three elements for specifying the modules: early, mid, and late.
Each element expects a numeric vector specifying the developmental stages
or experiments that correspond to each module. For example,
a character string specifying the legend title.
label of x-axis.
label of y-axis.
number of ticks that shall be drawn on the y-axis.
logical indicating whether or not the y-axis scale shall be adjusted to the same range in case two groups are specified. Default is
transparency of the shaded area (between [0,1]). Default is
place holder for old version of PlotRE that was based on base graphics instead of ggplot2.
a plot showing the relative expression profiles of phylostrata or divergence-strata belonging to the same group.
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.
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.
# read standard phylotranscriptomics data data(PhyloExpressionSetExample) data(DivergenceExpressionSetExample) # example PhyloExpressionSet PlotRE(PhyloExpressionSetExample, Groups = list(c(1:3), c(4:12)), legendName = "PS") # or you can choose any combination of groups PlotRE(PhyloExpressionSetExample, Groups = list(c(1,7,9), c(2:6,8,10:12)), legendName = "PS") # example DivergenceExpressionSet PlotRE(DivergenceExpressionSetExample, Groups = list(c(1:5), c(6:10)), legendName = "DS")