This function computes for each age category the corresponding mean expression profile.

PlotMeans(
ExpressionSet,
Groups = NULL,
modules = NULL,
legendName = "age",
xlab = "Ontogeny",
ylab = "Mean Expression Level",
main = "",
y.ticks = 10,
alpha = 0.008,
...
)

## Arguments

ExpressionSet 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, Groups = list(c(1:3), c(4:12)). The group options is limited to 2 Groups. 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. a character string specifying the legend title. label of x-axis. label of y-axis. main text. 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 adjust.range = TRUE. transparency of the shaded area (between [0,1]). Default is alpha = 0.1. place holder for old version of PlotMeans that was based on base graphics instead of ggplot2.

## Value

a plot showing mean expression profiles of each age category.

## Details

This plot may be useful to compare the absolute mean expression levels of each age category across stages.

In different developmental processes different phylostratum or divergence-stratum classes might be more expressed than others, hence contributing more to the overall phylotranscriptomics pattern (TAI or TDI). This plot can help to identify the phylostratum or divergence-stratum classes that contributes most to the overall transcriptome of the given developmental process.

PlotBarRE, RE, REMatrix, PlotRE

Hajk-Georg Drost

## Examples

### Example using a PhyloExpressionSet
### and DivergenceExpressionSet
data(PhyloExpressionSetExample)

data(DivergenceExpressionSetExample)

# plot evolutionary old PS (PS1-3) vs evolutionary young PS (PS4-12)
PlotMeans(PhyloExpressionSetExample,
Groups = list(c(1:3), c(4:12)),
legendName = "PS",

# if users wish to not adjust the y-axis scale when
# 2 groups are selected they can specify: adjust.range = FALSE
PlotMeans(PhyloExpressionSetExample,
Groups = list(c(1:3), c(4:12)),
legendName = "PS",