PlotSignature {myTAI} | R Documentation |
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.
|
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 |
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
)
Author(s)
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")