Plot Relative Expression Levels

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,
  ...
)

Arguments

ExpressionSet: a standard PhyloExpressionSet or DivergenceExpressionSet object.
Groups: 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, Groups = list(c(1:3), c(4:12)). The group options is limited to 2 Groups.
modules: 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, module = list(early = 1:2, mid = 3:5, late = 6:7) devides a dataset storing seven developmental stages into 3 modules. Default is modules = NULL. But if specified, a shaded are will be drawn to illustrate stages corresponding to the mid module.
legendName: a character string specifying the legend title.
xlab: label of x-axis.
ylab: label of y-axis.
main: main text.
y.ticks: number of ticks that shall be drawn on the y-axis.
adjust.range: logical indicating whether or not the y-axis scale shall be adjusted to the same range in case two groups are specified. Default is adjust.range = TRUE.
alpha: transparency of the shaded area (between [0,1]). Default is alpha = 0.1.
...: place holder for old version of PlotRE that was based on base graphics instead of ggplot2.

Value

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

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.

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.

Author

Hajk-Georg Drost

Examples


# 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")