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 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 |
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 |
y.ticks | number of ticks on the y-axis. 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
)
Hajk-Georg 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.![]()