PlotVars: Plot Variance of Expression Profiles

In drostlab/myTAI: Evolutionary Transcriptomics

Plot Variance of Expression Profiles

Description

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

Usage

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

Arguments

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

Details

This plot may be useful to compare the absolute variance 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.

Value

a plot showing variance expression profiles of each age category.

Author(s)

Hajk-Georg Drost

See Also

PlotBarRE, RE, REMatrix, PlotRE

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)
PlotVars(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
PlotVars(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!
PlotVars(DivergenceExpressionSetExample,
          Groups = list(c(1:5), c(6:10)), 
          legendName = "DS",
          adjust.range = TRUE)

drostlab/myTAI documentation built on April 8, 2024, 8:24 a.m.