Plot Mean Relative Expression Levels as Barplot

This function takes a PhyloExpressionSet or DivergenceExpressionSet object as input and computes for two or more defined phylostratum (divergence stratum) classes the statistical significance of the differences of mean relative expression of these two (or more) corresponding phylostratum (divergence stratum) classes. As test-statistic, the function performs a nonparametric kruskal.test based on relative expression values stored within each defined phylostratum class.

Usage

PlotBarRE(
  ExpressionSet,
  Groups = NULL,
  wLength = 0.1,
  ratio = FALSE,
  p.adjust.method = NULL,
  ...
)

Arguments

ExpressionSet: a standard PhyloExpressionSet or DivergenceExpressionSet object.
Groups: a list containing the phylostrata or divergence-strata that correspond to the same phylostratum class or divergence class. For ex. evolutionary old phylostrata: PS1-3 (Class 1) and evolutionary young phylostrata: PS4-12 (Class 2). In this case, the Groups list could be assigned as, Groups = list(c(1:3), c(4:12)). It is also possible to define more than 2 groups of evolutionary ages. For ex. Groups = list(c(1:3),c(4:8),c(9:12)) would perform a kruskal.test to determine the statistical significance of the evolutionary classes PS1-3, PS4-6, and PS9-12 based on their corresponding mean relative expression levels.
wLength: a numeric value defining the whiskers length above the bars. In case there are numerous different phylostratum classes a smaller wLength parameter should be used for better visualizations.
ratio: a boolean value specifying whether the bars in the barplot represent the mean relative expression level of phylostrata belonging to the same phylostratum class. In case ratio = TRUE, the ratio of the mean relative expression level of the two phylostrata classes is plotted as lines within the barplot. This parameter can only be used for 2 class comparisons.
p.adjust.method: correction method to adjust p-values for multiple comparisons (see p.adjust for possible methods). E.g., p.adjust.method = "BH" (Benjamini & Hochberg (1995)) or p.adjust.method = "bonferroni" (Bonferroni correction).
...: default graphics parameters.

Value

A barplot comparing Phylostratum-Classes by its mean relative expression levels. Significant stages are marked by '*' referring to statistically significant differences:

(1) '*' = P-Value <= 0.05

(2) '**' = P-Value <= 0.005

(3) '***' = P-Value <= 0.0005

Details

In case a large number of developmental stages is included in the input ExpressionSet, p-values returned by PlotBarRE should be adjusted for multiple comparisons which can be done by specifying the p.adjust.method argument.

References

Quint M et al. 2012. "A transcriptomic hourglass in plant embryogenesis". Nature (490): 98-101.

Domazet-Loso T. and Tautz D. 2010. "A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns". Nature (468): 815-818.

Myles Hollander and Douglas A. Wolfe (1973), Nonparametric Statistical Methods. New York: John Wiley & Sons. Pages 115-120.

Author

Hajk-Georg Drost

Examples


# read standard phylotranscriptomics data
data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)

# example PhyloExpressionSet
PlotBarRE(ExpressionSet = PhyloExpressionSetExample,
          Groups        = list(c(1:3), c(4:12)))



# example DivergenceExpressionSet
PlotBarRE(ExpressionSet = DivergenceExpressionSetExample,
          Groups        = list(c(1:5), c(6:10)))



# Perform PlotBarRE() with p-value adjustment method Benjamini & Hochberg (1995)
PlotBarRE(ExpressionSet   = PhyloExpressionSetExample,
          Groups          = list(c(1:3), c(4:12)),
          p.adjust.method = "BH")

       
             
# Example: plot ratio
# the ratio curve visualizes the ratio between bar 1 / bar 2
# the z - axis shows the corresponding ratio value of bar 1 / bar 2
PlotBarRE(ExpressionSet = PhyloExpressionSetExample,
          Groups        = list(c(1:3), c(4:12)),
          ratio         = TRUE)