myTAI (version 0.9.3)

PlotRE: Plot Relative Expression Levels

Description

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.

Usage

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.

See Also

PlotBarRE, RE, REMatrix

Examples

# NOT RUN {
# 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")


  
# }