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

PlotMedians(
ExpressionSet,
Groups = NULL,
legendName = "age",
xlab = "Ontogeny",
ylab = "Median Expression Level",
main = "",
y.ticks = 10,
adjust.range = TRUE
)

## Arguments

ExpressionSet a standard PhyloExpressionSet or DivergenceExpressionSet object. a list containing the age categories for which median 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 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.

## Value

a plot showing median expression profiles of each age category.

## Details

This plot may be useful to compare the absolute median 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.

## See also

PlotBarRE, RE, REMatrix, PlotRE

Hajk-Georg Drost

## Examples

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

# load PhyloExpressionSet
data(DivergenceExpressionSetExample)

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

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

# plot conserved DS (DS1-5) vs divergent DS (PS6-10)
# NOTE: DS are always defined in the range 1, 2, ... , 10.
# Hence, make sure that your groups are within this range!
PlotMedians(DivergenceExpressionSetExample,
Groups = list(c(1:5), c(6:10)),
legendName = "DS",
adjust.range = TRUE)