Main function to visualize transcriptome indices.
PlotSignature( ExpressionSet, measure = "TAI", TestStatistic = "FlatLineTest", modules = NULL, permutations = 1000, lillie.test = FALSE, p.value = TRUE, shaded.area = FALSE, custom.perm.matrix = NULL, xlab = "Ontogeny", ylab = "Transcriptome Index", main = "", lwd = 4, alpha = 0.1, y.ticks = 10 )
ExpressionSet  a standard PhyloExpressionSet, DivergenceExpressionSet or PolymorphismsExpressionSet object. 

measure  type of transcriptome index that shall be computed. E.g.

TestStatistic  a string defining the type of test statistics to be used to quantify the statistical significance the present phylotranscriptomics pattern. Possible values can be:

modules  a list storing three elements for the

permutations  a numeric value specifying the number of permutations to be performed for the 
lillie.test  a boolean value specifying whether the Lilliefors KolmogorovSmirnov Test shall be performed. 
p.value  a boolean value specifying whether the pvalue of the test statistic shall be printed within the plot area. 
shaded.area  a boolean value specifying whether a shaded area shall be drawn for the developmental stages defined to be the presumptive phylotypic period. 
custom.perm.matrix  a custom 
xlab  label of xaxis. 
ylab  label of yaxis. 
main  figure title. 
lwd  line width. 
alpha  transparency of the shaded area (between [0,1]). Default is 
y.ticks  number of ticks on the yaxis. Default is 
This function substitutes the functionality of the PlotPattern
function
and is based on ggplot2 insead of base R graphics.
The following transcriptome indices can be computed and visualized with this function:
Transcriptome Age Index (TAI
)
Transcriptome Divergence Index (TDI
)
Transcriptome Polymorphism Index (TPI
)
HajkGeorg Drost
data(PhyloExpressionSetExample) # plot TAI pattern and perform flat line test PlotSignature(PhyloExpressionSetExample, measure = "TAI", permutations = 100, TestStatistic = "FlatLineTest", ylab = "Transcriptome Age Index") #> Plot signature: ' TAI ' and test statistic: ' FlatLineTest ' running 100 permutations. #> Significance status of signature: significant.