myTAI (version 0.8.0)

PlotSignature: Plot evolutionary signatures across transcriptomes

Description

Main function to visualize transcriptome indices.

Usage

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)

Arguments

ExpressionSet

a standard PhyloExpressionSet, DivergenceExpressionSet or PolymorphismsExpressionSet object.

measure

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).

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: 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).

modules

a list storing three elements for the ReductiveHourglassTest or EarlyConservationTest: 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.

permutations

a numeric value specifying the number of permutations to be performed for the FlatLineTest, EarlyConservationTest or ReductiveHourglassTest.

lillie.test

a boolean value specifying whether the Lilliefors Kolmogorov-Smirnov Test shall be performed.

p.value

a boolean value specifying whether the p-value 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 bootMatrix (permutation matrix) to perform the underlying test statistic visualized by PlotPattern. Default is custom.perm.matrix = NULL.

xlab

label of x-axis.

ylab

label of y-axis.

main

figure title.

lwd

line width.

alpha

transparency of the shaded area (between [0,1]). Default is alpha = 0.1.

y.ticks

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)

Examples

# NOT RUN {
data(PhyloExpressionSetExample)

# plot TAI pattern and perform flat line test
PlotSignature(PhyloExpressionSetExample, 
              measure       = "TAI", 
              permutations  = 1000,
              TestStatistic = "FlatLineTest",
              ylab = "Transcriptome Age Index")
              
# plot TAI pattern and perform reductive hourglass test
PlotSignature(PhyloExpressionSetExample, 
              measure       = "TAI", 
              permutations  = 1000,
              TestStatistic = "ReductiveHourglassTest",
              modules       = list(early = 1:2, mid = 3:5, late = 6:7),
              ylab = "Transcriptome Age Index")
# }