Main function to visualize transcriptome indices.

PlotSignature(
ExpressionSet,
measure = "TAI",
TestStatistic = "FlatLineTest",
modules = NULL,
permutations = 1000,
lillie.test = FALSE,
p.value = TRUE,
custom.perm.matrix = NULL,
xlab = "Ontogeny",
ylab = "Transcriptome Index",
main = "",
lwd = 4,
alpha = 0.1,
y.ticks = 10
)

## Arguments

ExpressionSet a standard PhyloExpressionSet, DivergenceExpressionSet or PolymorphismsExpressionSet object. type of transcriptome index that shall be computed. E.g. measure = "TAI" (Transcriptome Age Index) measure = "TDI" (Transcriptome Divergence Index) measure = "TPI" (Transcriptome Polymorphism Index) a string defining the type of test statistics to be used to quantify the statistical significance the present phylotranscriptomics pattern. Possible values can be: TestStatistic = "FlatLineTest" : Statistical test for the deviation from a flat line TestStatistic = "ReductiveHourglassTest" : Statistical test for the existence of a hourglass shape (high-low-high pattern) TestStatistic = "EarlyConservationTest" : Statistical test for the existence of a earlyconservation pattern (low-high-high pattern) TestStatistic = "ReverseHourglassTest" : Statistical test for the existence of a reverse hourglass pattern (low-high-low pattern) a list storing three elements for the ReductiveHourglassTest, EarlyConservationTest, or ReverseHourglassTest: 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. a numeric value specifying the number of permutations to be performed for the FlatLineTest, EarlyConservationTest, ReductiveHourglassTest or ReverseHourglassTest. a boolean value specifying whether the Lilliefors Kolmogorov-Smirnov Test shall be performed. a boolean value specifying whether the p-value of the test statistic shall be printed within the plot area. a boolean value specifying whether a shaded area shall be drawn for the developmental stages defined to be the presumptive phylotypic period. a custom bootMatrix (permutation matrix) to perform the underlying test statistic visualized by PlotSignature. Default is custom.perm.matrix = NULL. label of x-axis. label of y-axis. figure title. line width. transparency of the shaded area (between [0,1]). Default is alpha = 0.1. number of ticks on the y-axis. Default is ticks = 10.

## Details

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)

Hajk-Georg Drost

## Examples

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.