PlotSignatureMultiple: Plot evolutionary signatures across transcriptomes, for...

In drostlab/myTAI: Evolutionary Transcriptomics

Plot evolutionary signatures across transcriptomes, for multiple expression sets

Description

PlotSignatureMultiple is used to compare multiple transcriptomic index profiles (e.g. TAI) over a common process of interest (e.g. a developmental process). The main use case is visualising how removing different subsets of genes from the expression set can perturb the transcriptome index signal.

Usage

PlotSignatureMultiple(
  ExpressionSets,
  set.labels,
  measure = "TAI",
  TestStatistic = "FlatLineTest",
  modules = NULL,
  permutations = 1000,
  p.value = TRUE,
  shaded.area = FALSE,
  xlab = "Ontogeny",
  ylab = "Transcriptome Index",
  main = "",
  legend.title = "Expression Sets",
  lwd = 4,
  alpha = 0.1,
  y.ticks = 3
)

Arguments

ExpressionSets	a list of PhyloExpressionSet, DivergenceExpressionSet or PolymorphismsExpressionSet objects.
set.labels	a character vector of labels, one for each given expression set
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 = "ReverseHourglassTest" : Statistical test for the existence of a reverse hourglass pattern (low-high-low pattern) TestStatistic = "EarlyConservationTest" : Statistical test for the existence of a early conservation pattern (low-high-high pattern) TestStatistic = "LateConservationTest" : Statistical test for the existence of a late conservation pattern (high-high-low pattern)
modules	a list storing three elements for the ReductiveHourglassTest, EarlyConservationTest, LateConservationTest, 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: modules = list(early = 1:2, mid = 3:5, late = 6:7) divides 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, LateConservationTest, ReductiveHourglassTest or ReverseHourglassTest.
p.value	a boolean value specifying whether the p-value of the test statistic shall be printed within the legend, for each expression set.
shaded.area	a boolean value specifying whether a shaded area shall be drawn for the developmental stages defined to be the presumptive phylotypic period.
xlab	label of x-axis.
ylab	label of y-axis.
main	figure title.
legend.title	legend title.
lwd	line width.
alpha	transparency of the shaded area and error ribbon (between [0,1]). Default is alpha = 0.1.
y.ticks	number of ticks on the y-axis. Default is ticks = 3.

Value

a ggplot object visualising the transcriptome index of each given expression set, together with its standard deviation per stage, obtained by permuting the gene ages. The profiles are shown on the same axes, so that they can be readily compared. Optionally, the p-value of each profile, with respect to the choice of statistic, is shown.

Author(s)

Stefan Manolache

Examples

data(PhyloExpressionSetExample)

# remove top 1% expressed genes
genes.top_expression <- TopExpressionGenes(PhyloExpressionSetExample, p=.99)
PhyloExpressionSetExample.top_removed <- subset(PhyloExpressionSetExample, 
                                        !(GeneID %in% genes.top_expression))

expression_sets = list(PhyloExpressionSetExample, PhyloExpressionSetExample.top_removed)
set_labels = c("100%", "99%")

# Flat line test
PlotSignatureMultiple(ExpressionSets = expression_sets,
                      set.labels = set_labels,
                      TestStatistic="FlatLineTest",
                      main = "A. thaliana embryogenesis",
                      legend.title = "Top Expressed Genes Quantile")
                      
# Reductive hourglass test
PlotSignatureMultiple(ExpressionSets = expression_sets,
                      set.labels = set_labels,
                      TestStatistic="ReductiveHourglassTest",
                      main = "A. thaliana embryogenesis",
                      legend.title = "Top Expressed Genes Quantile",
                      modules=list(early=1:2, mid=3:5, late=6:7),
                      shaded.area=TRUE)                                                        

drostlab/myTAI documentation built on Feb. 15, 2025, 6:44 p.m.