vignettes/Introduction.R
In HajkD/myTAI: Evolutionary Transcriptomics
## ---- echo = FALSE, message = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
library(myTAI)
options(width = 750)
knitr::opts_chunk$set(
comment = "#>",
error = FALSE,
tidy = FALSE)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # load myTAI
# library(myTAI)
#
# # load example data sets (stored in myTAI)
# data(PhyloExpressionSetExample)
# data(DivergenceExpressionSetExample)
#
# # show an example phylostratigraphic map of Arabidopsis thaliana
# head(PhyloExpressionSetExample[ , c("Phylostratum","GeneID")])
#
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # show an example structure of a Divergence Map
# head(DivergenceExpressionSetExample[ , c("Divergence.stratum","GeneID")])
#
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# library(myTAI)
#
# # load the example data set
# data(PhyloExpressionSetExample)
#
# # construct an example Phylostratigraphic Map
# Example.PhylostratigraphicMap <- PhyloExpressionSetExample[ , 1:2]
# # construct an example ExpressionMatrix
# Example.ExpressionMatrix <- PhyloExpressionSetExample[ , 2:9]
#
# # join a PhylostratigraphicMap with an ExpressionMatrix using MatchMap()
# Example.PhyloExpressionSet <- MatchMap(Example.PhylostratigraphicMap, Example.ExpressionMatrix)
#
# # look at a standard PhyloExpressionSet
# head(Example.PhyloExpressionSet, 3)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # head of an example standard DivergenceExpressionSet
# head(DivergenceExpressionSetExample, 3)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # used by all myTAI functions to check the validity of the PhyloExpressionSet standard
# is.ExpressionSet(PhyloExpressionSetExample)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # used a non standard PhyloExpressionSet
# head(PhyloExpressionSetExample[ , 2:5], 2)
## ---- error = TRUE,eval=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# is.ExpressionSet(PhyloExpressionSetExample[ , 2:5])
## ---- eval = FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # convert any tibble to a data.frame
# PhyloExpressionSetExample <- as.data.frame(PhyloExpressionSetExample)
# # now is.ExpressionSet() should return TRUE
# is.ExpressionSet(PhyloExpressionSetExample)
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(PhyloExpressionSetExample)
# # Plot the Transcriptome Age Index of a given PhyloExpressionSet
# # Test Statistic : Flat Line Test (default)
# PlotSignature( ExpressionSet = PhyloExpressionSetExample,
# measure = "TAI",
# TestStatistic = "FlatLineTest",
# xlab = "Ontogeny",
# ylab = "TAI" )
## ---- fig.width= 9, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(PhyloExpressionSetExample)
# # category-centered visualization of PS
# # specific expression level distributions (log-scale)
# PlotCategoryExpr(ExpressionSet = PhyloExpressionSetExample,
# legendName = "PS",
# test.stat = TRUE,
# type = "category-centered",
# distr.type = "boxplot",
# log.expr = TRUE)
## ---- fig.width= 9, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(PhyloExpressionSetExample)
# # plot evolutionary old PS (PS1-3) vs
# # evolutionary young PS (PS4-12)
# PlotMeans(PhyloExpressionSetExample,
# Groups = list(c(1:3), c(4:12)),
# legendName = "PS",
# adjust.range = TRUE)
## ---- fig.width= 9, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(PhyloExpressionSetExample)
# # plot evolutionary old PS (PS1-3) vs
# # evolutionary young PS (PS4-12)
# PlotRE(PhyloExpressionSetExample,
# Groups = list(c(1:3), c(4:12)),
# legendName = "PS",
# adjust.range = TRUE)
## ----eval=FALSE,echo=FALSE,fig.width= 7, fig.height= 15---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # select PS4-12 genes
# PhyloExpressionSetExample.PS4_12 <-
# dplyr::filter(PhyloExpressionSetExample, Phylostratum %in% c(4:12))
# # categorize A. thaliana embryogenesis into three
# # developmental modules (early, mid, and late)
# Ath.Embryogenesis.DiffGenes <-
# DiffGenes(
# ExpressionSet = PhyloExpressionSetExample.PS4_12,
# nrep = c(2, 3, 2),
# stage.names = c("Early", "Mid", "Late")
# )
#
# # cluster young genes (PS4-12) according to their fold-change pattern: High-Low-Low
# Ath.Embryo.High_Low_Low <-
# PhyloExpressionSetExample.PS4_12[which((Ath.Embryogenesis.DiffGenes[, "Early->Mid"] > 3) &
# (dplyr::between(Ath.Embryogenesis.DiffGenes[, "Mid->Late"], 1, 2))),]
#
# # cluster young genes (PS4-12) according to their fold-change pattern: High-Low-High
# Ath.Embryo.High_Low_High <-
# PhyloExpressionSetExample.PS4_12[which((Ath.Embryogenesis.DiffGenes[, "Early->Mid"] > 3) &
# (Ath.Embryogenesis.DiffGenes[, "Mid->Late"] < 0.2)),]
#
# # cluster young genes (PS4-12) according to their fold-change pattern: Low-Low-High
# Ath.Embryo.Low_Low_High <-
# PhyloExpressionSetExample.PS4_12[which((dplyr::between(Ath.Embryogenesis.DiffGenes[, "Early->Mid"], 1, 2)) &
# (Ath.Embryogenesis.DiffGenes[, "Mid->Late"] < 0.2)),]
#
#
# par(mfrow = c(3, 1))
# matplot(
# t(Ath.Embryo.High_Low_Low[, 3:9]),
# type = "l",
# lty = 1,
# lwd = 2,
# col = "lightblue",
# xlab = "Ontogeny",
# ylab = "Expression Level",
# xaxt = "n",
# cex.lab = 1.5,
# cex.axis = 1.5,
# main = "High-Low-Low"
# )
# lines(
# colMeans(Ath.Embryo.High_Low_Low[, 3:9]),
# lwd = 6 ,
# col = "red",
# cex.lab = 1.5,
# cex.axis = 1.5,
# cex = 1.5
# )
# axis(1, 1:7, names(PhyloExpressionSetExample)[3:9])
# text(
# 4,
# max(Ath.Embryo.High_Low_Low[, 3:9]) - 6000,
# labels = paste0(nrow(Ath.Embryo.High_Low_Low), " Genes"),
# cex = 2
# )
#
# matplot(
# t(Ath.Embryo.High_Low_High[, 3:9]),
# type = "l",
# lty = 1,
# lwd = 2,
# col = "lightblue",
# xlab = "Ontogeny",
# ylab = "Expression Level",
# xaxt = "n",
# cex.lab = 1.5,
# cex.axis = 1.5,
# main = "High-Low-High"
# )
# lines(
# colMeans(Ath.Embryo.High_Low_High[, 3:9]),
# lwd = 6 ,
# col = "red",
# cex.lab = 1.5,
# cex.axis = 1.5,
# cex = 1.5
# )
# axis(1, 1:7, names(PhyloExpressionSetExample)[3:9])
# text(
# 4,
# max(Ath.Embryo.High_Low_High[, 3:9]) - 6000,
# labels = paste0(nrow(Ath.Embryo.High_Low_High), " Genes"),
# cex = 2
# )
#
# matplot(
# t(Ath.Embryo.Low_Low_High[, 3:9]),
# type = "l",
# lty = 1,
# lwd = 2,
# col = "lightblue",
# xlab = "Ontogeny",
# ylab = "Expression Level",
# xaxt = "n",
# cex.lab = 1.5,
# cex.axis = 1.5,
# main = "Low-Low-High"
# )
# lines(
# colMeans(Ath.Embryo.Low_Low_High[, 3:9]),
# lwd = 6 ,
# col = "red",
# cex.lab = 1.5,
# cex.axis = 1.5,
# cex = 1.5
# )
# axis(1, 1:7, names(PhyloExpressionSetExample)[3:9])
# text(
# 4,
# max(Ath.Embryo.Low_Low_High[, 3:9]) - 6000,
# labels = paste0(nrow(Ath.Embryo.Low_Low_High), " Genes"),
# cex = 2
# )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(PhyloExpressionSetExample)
# # Plot the Transcriptome Age Index of a given PhyloExpressionSet
# # Test Statistic : Flat Line Test (default)
# PlotSignature( ExpressionSet = PhyloExpressionSetExample,
# measure = "TAI",
# TestStatistic = "FlatLineTest",
# xlab = "Ontogeny",
# ylab = "TAI" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Plot the Transcriptome Age Index of a given PhyloExpressionSet
# # Test Statistic : Reductive Hourglass Test
# PlotSignature( ExpressionSet = PhyloExpressionSetExample,
# measure = "TAI",
# TestStatistic = "ReductiveHourglassTest",
# modules = list(early = 1:2, mid = 3:5, late = 6:7),
# xlab = "Ontogeny",
# ylab = "TAI" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualize the phylotypic period used for the Reductive Hourglass Test
# PlotSignature( ExpressionSet = PhyloExpressionSetExample,
# measure = "TAI",
# TestStatistic = "ReductiveHourglassTest",
# modules = list(early = 1:2, mid = 3:5, late = 6:7),
# shaded.area = TRUE,
# xlab = "Ontogeny",
# ylab = "TAI" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Plot the Transcriptome Age Index of a given PhyloExpressionSet
# # Test Statistic : Reductive Early Conservation Test
# PlotSignature( ExpressionSet = PhyloExpressionSetExample,
# measure = "TAI",
# TestStatistic = "EarlyConservationTest",
# modules = list(early = 1:2, mid = 3:5, late = 6:7),
# xlab = "Ontogeny",
# ylab = "TAI" )
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Compute the Transcriptome Age Index values of a given PhyloExpressionSet
# TAI(PhyloExpressionSetExample)
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Plot the Transcriptome Age Index of a given PhyloExpressionSet
# # Test Statistic : Reverse Hourglass Test
# PlotSignature( ExpressionSet = PhyloExpressionSetExample,
# measure = "TAI",
# TestStatistic = "ReverseHourglassTest",
# modules = list(early = 1:2, mid = 3:5, late = 6:7),
# xlab = "Ontogeny",
# ylab = "TAI" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualize the phylotypic period used for the Reductive Hourglass Test
# PlotSignature( ExpressionSet = PhyloExpressionSetExample,
# measure = "TAI",
# TestStatistic = "ReverseHourglassTest",
# modules = list(early = 1:2, mid = 3:5, late = 6:7),
# shaded.area = TRUE,
# xlab = "Ontogeny",
# ylab = "TAI" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(DivergenceExpressionSetExample)
# # Plot the Transcriptome Divergence Index of a given DivergenceExpressionSet
# # Test Statistic : Flat Line Test (default)
# PlotSignature( ExpressionSet = DivergenceExpressionSetExample,
# measure = "TDI",
# TestStatistic = "FlatLineTest",
# xlab = "Ontogeny",
# ylab = "TDI" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(DivergenceExpressionSetExample)
# # Plot the Transcriptome Divergence Index of a given DivergenceExpressionSet
# # Test Statistic : Reductive Hourglass Test
# PlotSignature( ExpressionSet = DivergenceExpressionSetExample,
# measure = "TDI",
# TestStatistic = "ReductiveHourglassTest",
# modules = list(early = 1:2, mid = 3:5, late = 6:7),
# xlab = "Ontogeny",
# ylab = "TDI" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(DivergenceExpressionSetExample)
# # Plot the Transcriptome Divergence Index of a given DivergenceExpressionSet
# # Test Statistic : Reductive Early Conservation Test
# PlotSignature( ExpressionSet = DivergenceExpressionSetExample,
# measure = "TDI",
# TestStatistic = "EarlyConservationTest",
# modules = list(early = 1:2, mid = 3:5, late = 6:7),
# xlab = "Ontogeny",
# ylab = "TDI" )
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Compute the Transcriptome Divergence Index values of a given DivergenceExpressionSet
# TDI(DivergenceExpressionSetExample)
## ---- fig.width= 7, fig.height= 5, eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(PhyloExpressionSetExample)
# # visualize phylostrata contribution to the global TAI pattern
# PlotContribution( ExpressionSet = PhyloExpressionSetExample,
# legendName = "PS",
# xlab = "Ontogeny",
# ylab = "Transcriptome Age Index",
# y.ticks = 10)
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# pTAI(PhyloExpressionSetExample)
## ---- fig.width= 7, fig.height= 5, eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(DivergenceExpressionSetExample)
# # visualize divergence stratum contribution to global TDI
# PlotContribution( ExpressionSet = DivergenceExpressionSetExample,
# legendName = "DS")
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# pTDI(DivergenceExpressionSetExample)
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # show that the cumulative TAI value of PS 12 is
# # equivalent to the global TAI() values
# pTAI(PhyloExpressionSetExample)[12 , ]
#
# # > Zygote Quadrant Globular Heart Torpedo Bent Mature
# # > 3.229942 3.225614 3.107135 3.116693 3.073993 3.176511 3.390334
#
# TAI(PhyloExpressionSetExample)
#
# # > Zygote Quadrant Globular Heart Torpedo Bent Mature
# # > 3.229942 3.225614 3.107135 3.116693 3.073993 3.176511 3.390334
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # show that the colSum() of partial TAI values
# # over all Phylostrata equals the global TAI() values
# apply(pStrata(PhyloExpressionSetExample) , 2 , sum)
#
# # > Zygote Quadrant Globular Heart Torpedo Bent Mature
# # > 3.229942 3.225614 3.107135 3.116693 3.073993 3.176511 3.390334
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # show that apply(pStrata(PhyloExpressionSetExample) , 2 , cumsum)
# # is equivalent to pTAI()
# apply(pStrata(PhyloExpressionSetExample) , 2 , cumsum)
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# pTAI(PhyloExpressionSetExample)
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # compute partial TAI values for each Phylostratum
# pStrata(PhyloExpressionSetExample)
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # compute partial TAI values for each gene
# dplyr::glimpse(pMatrix(PhyloExpressionSetExample))
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean gene expression of each Phylostratum class
# PlotMeans( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(1:12),
# legendName = "PS")
## ---- fig.height= 5, fig.width=7,eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean gene expression of each Phylostratum class
# # in two separate plots (groups)
# PlotMeans( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(group_1 = 1:3, group_2 = 4:12),
# legendName = "PS")
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Using the age.apply() function to compute the mean expression levels
# # of all Phylostrata
# age.apply( ExpressionSet = PhyloExpressionSetExample,
# FUN = colMeans )
## ---- fig.height= 5, fig.width=7,eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean gene expression of each Phylostratum class
# # and draw an shaded area for the mid-module.
# PlotMeans( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(1:12),
# modules = list(1:2,3:5,6:7),
# legendName = "PS")
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(DivergenceExpressionSetExample)
# # Visualizing the mean gene expression of each Divergence Stratum class
# PlotMeans( ExpressionSet = DivergenceExpressionSetExample,
# Groups = list(1:10),
# legendName = "DS",
# xlab = "Ontogeny")
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Using the age.apply() function to compute the mean expression levels
# # of all Divergence Strata
# age.apply( ExpressionSet = DivergenceExpressionSetExample,
# FUN = colMeans )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean gene expression of each Phylostratum class
# PlotRE( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(1:12),
# legendName = "PS",
# xlab = "Ontogeny")
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(DivergenceExpressionSetExample)
# # Visualizing the mean gene expression of each Divergence Stratum class
# PlotRE( ExpressionSet = DivergenceExpressionSetExample,
# Groups = list(1:10),
# legendName = "DS",
# xlab = "Ontogeny")
## ----fig.height=5, fig.width=7,eval=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean gene expression of each Phylostratum class
# PlotRE( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(group_1 = 1:3, group_2 = 4:12),
# legendName = "PS",
# xlab = "Ontogeny")
## ----fig.height=5, fig.width=7,eval=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean gene expression of each Phylostratum class
# PlotRE( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(1:12),
# modules = list(1:2,3:5,6:7),
# legendName = "PS",
# xlab = "Ontogeny")
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Getting the relative expression levels for all Phylostrata
# REMatrix(PhyloExpressionSetExample)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Getting the relative expression levels for all Divergence-Strata
# REMatrix(DivergenceExpressionSetExample)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Getting the relative expression levels for all Phylostrata
# age.apply( ExpressionSet = PhyloExpressionSetExample,
# FUN = RE )
## ----fig.height=5, fig.width=7,eval=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean relative expression of two Phylostratum groups
# PlotBarRE( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(group_1 = 1:3, group_2 = 4:12),
# xlab = "Ontogeny",
# ylab = "Mean Relative Expression",
# cex = 1.5)
## ---- fig.height=5,fig.width=7,eval=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean relative expression of two Phylostratum groups
# PlotBarRE( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(group_1 = 1:3, group_2 = 4:12),
# ratio = TRUE,
# xlab = "Ontogeny",
# ylab = "Mean Relative Expression",
# cex = 1.5 )
## ---- fig.width=7,eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean relative expression of three Phylostratum groups
# PlotBarRE( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(group_1 = 1:3, group_2 = 4:6, group_3 = 7:12),
# wLength = 0.05,
# xlab = "Ontogeny",
# ylab = "Mean Relative Expression",
# cex = 1.5 )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Display the phylostratum distribution (gene frequency distribution)
# # of a PhyloExpressionSet as absolute frequency distribution
# PlotDistribution( PhyloExpressionSet = PhyloExpressionSetExample,
# xlab = "Phylostratum" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Plot phylostrata as relative frequency distribution
# PlotDistribution( PhyloExpressionSet = PhyloExpressionSetExample,
# as.ratio = TRUE,
# xlab = "Phylostratum")
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#
# # save the TAI profile to a local machine with png()
# png("ExampleTAIProfile.png", width = 800, height = 600)
#
# PlotPattern( ExpressionSet = PhyloExpressionSetExample,
# type = "l",
# lwd = 6,
# xlab = "Ontogeny",
# ylab = "TAI",
# cex = 1,
# cex.lab = 1,
# cex.axis = 1.2 )
#
# dev.off()
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # store ggplot2 graphic in variable p
# p <- PlotSignature(ExpressionSet = PhyloExpressionSetExample,
# ylab = "Transcriptome Age Index")
#
# # save ggplot2 based TAI profile to a local machine with save_plot()
# cowplot::save_plot("ExampleTAIProfile.pdf",
# p,
# base_height = 8,
# base_width = 12 )
HajkD/myTAI documentation built on April 6, 2024, 7:47 p.m.
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## ---- echo = FALSE, message = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
library(myTAI)
options(width = 750)
knitr::opts_chunk$set(
comment = "#>",
error = FALSE,
tidy = FALSE)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # load myTAI
# library(myTAI)
#
# # load example data sets (stored in myTAI)
# data(PhyloExpressionSetExample)
# data(DivergenceExpressionSetExample)
#
# # show an example phylostratigraphic map of Arabidopsis thaliana
# head(PhyloExpressionSetExample[ , c("Phylostratum","GeneID")])
#
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # show an example structure of a Divergence Map
# head(DivergenceExpressionSetExample[ , c("Divergence.stratum","GeneID")])
#
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# library(myTAI)
#
# # load the example data set
# data(PhyloExpressionSetExample)
#
# # construct an example Phylostratigraphic Map
# Example.PhylostratigraphicMap <- PhyloExpressionSetExample[ , 1:2]
# # construct an example ExpressionMatrix
# Example.ExpressionMatrix <- PhyloExpressionSetExample[ , 2:9]
#
# # join a PhylostratigraphicMap with an ExpressionMatrix using MatchMap()
# Example.PhyloExpressionSet <- MatchMap(Example.PhylostratigraphicMap, Example.ExpressionMatrix)
#
# # look at a standard PhyloExpressionSet
# head(Example.PhyloExpressionSet, 3)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # head of an example standard DivergenceExpressionSet
# head(DivergenceExpressionSetExample, 3)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # used by all myTAI functions to check the validity of the PhyloExpressionSet standard
# is.ExpressionSet(PhyloExpressionSetExample)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # used a non standard PhyloExpressionSet
# head(PhyloExpressionSetExample[ , 2:5], 2)
## ---- error = TRUE,eval=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# is.ExpressionSet(PhyloExpressionSetExample[ , 2:5])
## ---- eval = FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # convert any tibble to a data.frame
# PhyloExpressionSetExample <- as.data.frame(PhyloExpressionSetExample)
# # now is.ExpressionSet() should return TRUE
# is.ExpressionSet(PhyloExpressionSetExample)
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(PhyloExpressionSetExample)
# # Plot the Transcriptome Age Index of a given PhyloExpressionSet
# # Test Statistic : Flat Line Test (default)
# PlotSignature( ExpressionSet = PhyloExpressionSetExample,
# measure = "TAI",
# TestStatistic = "FlatLineTest",
# xlab = "Ontogeny",
# ylab = "TAI" )
## ---- fig.width= 9, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(PhyloExpressionSetExample)
# # category-centered visualization of PS
# # specific expression level distributions (log-scale)
# PlotCategoryExpr(ExpressionSet = PhyloExpressionSetExample,
# legendName = "PS",
# test.stat = TRUE,
# type = "category-centered",
# distr.type = "boxplot",
# log.expr = TRUE)
## ---- fig.width= 9, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(PhyloExpressionSetExample)
# # plot evolutionary old PS (PS1-3) vs
# # evolutionary young PS (PS4-12)
# PlotMeans(PhyloExpressionSetExample,
# Groups = list(c(1:3), c(4:12)),
# legendName = "PS",
# adjust.range = TRUE)
## ---- fig.width= 9, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(PhyloExpressionSetExample)
# # plot evolutionary old PS (PS1-3) vs
# # evolutionary young PS (PS4-12)
# PlotRE(PhyloExpressionSetExample,
# Groups = list(c(1:3), c(4:12)),
# legendName = "PS",
# adjust.range = TRUE)
## ----eval=FALSE,echo=FALSE,fig.width= 7, fig.height= 15---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # select PS4-12 genes
# PhyloExpressionSetExample.PS4_12 <-
# dplyr::filter(PhyloExpressionSetExample, Phylostratum %in% c(4:12))
# # categorize A. thaliana embryogenesis into three
# # developmental modules (early, mid, and late)
# Ath.Embryogenesis.DiffGenes <-
# DiffGenes(
# ExpressionSet = PhyloExpressionSetExample.PS4_12,
# nrep = c(2, 3, 2),
# stage.names = c("Early", "Mid", "Late")
# )
#
# # cluster young genes (PS4-12) according to their fold-change pattern: High-Low-Low
# Ath.Embryo.High_Low_Low <-
# PhyloExpressionSetExample.PS4_12[which((Ath.Embryogenesis.DiffGenes[, "Early->Mid"] > 3) &
# (dplyr::between(Ath.Embryogenesis.DiffGenes[, "Mid->Late"], 1, 2))),]
#
# # cluster young genes (PS4-12) according to their fold-change pattern: High-Low-High
# Ath.Embryo.High_Low_High <-
# PhyloExpressionSetExample.PS4_12[which((Ath.Embryogenesis.DiffGenes[, "Early->Mid"] > 3) &
# (Ath.Embryogenesis.DiffGenes[, "Mid->Late"] < 0.2)),]
#
# # cluster young genes (PS4-12) according to their fold-change pattern: Low-Low-High
# Ath.Embryo.Low_Low_High <-
# PhyloExpressionSetExample.PS4_12[which((dplyr::between(Ath.Embryogenesis.DiffGenes[, "Early->Mid"], 1, 2)) &
# (Ath.Embryogenesis.DiffGenes[, "Mid->Late"] < 0.2)),]
#
#
# par(mfrow = c(3, 1))
# matplot(
# t(Ath.Embryo.High_Low_Low[, 3:9]),
# type = "l",
# lty = 1,
# lwd = 2,
# col = "lightblue",
# xlab = "Ontogeny",
# ylab = "Expression Level",
# xaxt = "n",
# cex.lab = 1.5,
# cex.axis = 1.5,
# main = "High-Low-Low"
# )
# lines(
# colMeans(Ath.Embryo.High_Low_Low[, 3:9]),
# lwd = 6 ,
# col = "red",
# cex.lab = 1.5,
# cex.axis = 1.5,
# cex = 1.5
# )
# axis(1, 1:7, names(PhyloExpressionSetExample)[3:9])
# text(
# 4,
# max(Ath.Embryo.High_Low_Low[, 3:9]) - 6000,
# labels = paste0(nrow(Ath.Embryo.High_Low_Low), " Genes"),
# cex = 2
# )
#
# matplot(
# t(Ath.Embryo.High_Low_High[, 3:9]),
# type = "l",
# lty = 1,
# lwd = 2,
# col = "lightblue",
# xlab = "Ontogeny",
# ylab = "Expression Level",
# xaxt = "n",
# cex.lab = 1.5,
# cex.axis = 1.5,
# main = "High-Low-High"
# )
# lines(
# colMeans(Ath.Embryo.High_Low_High[, 3:9]),
# lwd = 6 ,
# col = "red",
# cex.lab = 1.5,
# cex.axis = 1.5,
# cex = 1.5
# )
# axis(1, 1:7, names(PhyloExpressionSetExample)[3:9])
# text(
# 4,
# max(Ath.Embryo.High_Low_High[, 3:9]) - 6000,
# labels = paste0(nrow(Ath.Embryo.High_Low_High), " Genes"),
# cex = 2
# )
#
# matplot(
# t(Ath.Embryo.Low_Low_High[, 3:9]),
# type = "l",
# lty = 1,
# lwd = 2,
# col = "lightblue",
# xlab = "Ontogeny",
# ylab = "Expression Level",
# xaxt = "n",
# cex.lab = 1.5,
# cex.axis = 1.5,
# main = "Low-Low-High"
# )
# lines(
# colMeans(Ath.Embryo.Low_Low_High[, 3:9]),
# lwd = 6 ,
# col = "red",
# cex.lab = 1.5,
# cex.axis = 1.5,
# cex = 1.5
# )
# axis(1, 1:7, names(PhyloExpressionSetExample)[3:9])
# text(
# 4,
# max(Ath.Embryo.Low_Low_High[, 3:9]) - 6000,
# labels = paste0(nrow(Ath.Embryo.Low_Low_High), " Genes"),
# cex = 2
# )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(PhyloExpressionSetExample)
# # Plot the Transcriptome Age Index of a given PhyloExpressionSet
# # Test Statistic : Flat Line Test (default)
# PlotSignature( ExpressionSet = PhyloExpressionSetExample,
# measure = "TAI",
# TestStatistic = "FlatLineTest",
# xlab = "Ontogeny",
# ylab = "TAI" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Plot the Transcriptome Age Index of a given PhyloExpressionSet
# # Test Statistic : Reductive Hourglass Test
# PlotSignature( ExpressionSet = PhyloExpressionSetExample,
# measure = "TAI",
# TestStatistic = "ReductiveHourglassTest",
# modules = list(early = 1:2, mid = 3:5, late = 6:7),
# xlab = "Ontogeny",
# ylab = "TAI" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualize the phylotypic period used for the Reductive Hourglass Test
# PlotSignature( ExpressionSet = PhyloExpressionSetExample,
# measure = "TAI",
# TestStatistic = "ReductiveHourglassTest",
# modules = list(early = 1:2, mid = 3:5, late = 6:7),
# shaded.area = TRUE,
# xlab = "Ontogeny",
# ylab = "TAI" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Plot the Transcriptome Age Index of a given PhyloExpressionSet
# # Test Statistic : Reductive Early Conservation Test
# PlotSignature( ExpressionSet = PhyloExpressionSetExample,
# measure = "TAI",
# TestStatistic = "EarlyConservationTest",
# modules = list(early = 1:2, mid = 3:5, late = 6:7),
# xlab = "Ontogeny",
# ylab = "TAI" )
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Compute the Transcriptome Age Index values of a given PhyloExpressionSet
# TAI(PhyloExpressionSetExample)
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Plot the Transcriptome Age Index of a given PhyloExpressionSet
# # Test Statistic : Reverse Hourglass Test
# PlotSignature( ExpressionSet = PhyloExpressionSetExample,
# measure = "TAI",
# TestStatistic = "ReverseHourglassTest",
# modules = list(early = 1:2, mid = 3:5, late = 6:7),
# xlab = "Ontogeny",
# ylab = "TAI" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualize the phylotypic period used for the Reductive Hourglass Test
# PlotSignature( ExpressionSet = PhyloExpressionSetExample,
# measure = "TAI",
# TestStatistic = "ReverseHourglassTest",
# modules = list(early = 1:2, mid = 3:5, late = 6:7),
# shaded.area = TRUE,
# xlab = "Ontogeny",
# ylab = "TAI" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(DivergenceExpressionSetExample)
# # Plot the Transcriptome Divergence Index of a given DivergenceExpressionSet
# # Test Statistic : Flat Line Test (default)
# PlotSignature( ExpressionSet = DivergenceExpressionSetExample,
# measure = "TDI",
# TestStatistic = "FlatLineTest",
# xlab = "Ontogeny",
# ylab = "TDI" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(DivergenceExpressionSetExample)
# # Plot the Transcriptome Divergence Index of a given DivergenceExpressionSet
# # Test Statistic : Reductive Hourglass Test
# PlotSignature( ExpressionSet = DivergenceExpressionSetExample,
# measure = "TDI",
# TestStatistic = "ReductiveHourglassTest",
# modules = list(early = 1:2, mid = 3:5, late = 6:7),
# xlab = "Ontogeny",
# ylab = "TDI" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(DivergenceExpressionSetExample)
# # Plot the Transcriptome Divergence Index of a given DivergenceExpressionSet
# # Test Statistic : Reductive Early Conservation Test
# PlotSignature( ExpressionSet = DivergenceExpressionSetExample,
# measure = "TDI",
# TestStatistic = "EarlyConservationTest",
# modules = list(early = 1:2, mid = 3:5, late = 6:7),
# xlab = "Ontogeny",
# ylab = "TDI" )
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Compute the Transcriptome Divergence Index values of a given DivergenceExpressionSet
# TDI(DivergenceExpressionSetExample)
## ---- fig.width= 7, fig.height= 5, eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(PhyloExpressionSetExample)
# # visualize phylostrata contribution to the global TAI pattern
# PlotContribution( ExpressionSet = PhyloExpressionSetExample,
# legendName = "PS",
# xlab = "Ontogeny",
# ylab = "Transcriptome Age Index",
# y.ticks = 10)
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# pTAI(PhyloExpressionSetExample)
## ---- fig.width= 7, fig.height= 5, eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(DivergenceExpressionSetExample)
# # visualize divergence stratum contribution to global TDI
# PlotContribution( ExpressionSet = DivergenceExpressionSetExample,
# legendName = "DS")
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# pTDI(DivergenceExpressionSetExample)
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # show that the cumulative TAI value of PS 12 is
# # equivalent to the global TAI() values
# pTAI(PhyloExpressionSetExample)[12 , ]
#
# # > Zygote Quadrant Globular Heart Torpedo Bent Mature
# # > 3.229942 3.225614 3.107135 3.116693 3.073993 3.176511 3.390334
#
# TAI(PhyloExpressionSetExample)
#
# # > Zygote Quadrant Globular Heart Torpedo Bent Mature
# # > 3.229942 3.225614 3.107135 3.116693 3.073993 3.176511 3.390334
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # show that the colSum() of partial TAI values
# # over all Phylostrata equals the global TAI() values
# apply(pStrata(PhyloExpressionSetExample) , 2 , sum)
#
# # > Zygote Quadrant Globular Heart Torpedo Bent Mature
# # > 3.229942 3.225614 3.107135 3.116693 3.073993 3.176511 3.390334
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # show that apply(pStrata(PhyloExpressionSetExample) , 2 , cumsum)
# # is equivalent to pTAI()
# apply(pStrata(PhyloExpressionSetExample) , 2 , cumsum)
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# pTAI(PhyloExpressionSetExample)
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # compute partial TAI values for each Phylostratum
# pStrata(PhyloExpressionSetExample)
## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # compute partial TAI values for each gene
# dplyr::glimpse(pMatrix(PhyloExpressionSetExample))
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean gene expression of each Phylostratum class
# PlotMeans( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(1:12),
# legendName = "PS")
## ---- fig.height= 5, fig.width=7,eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean gene expression of each Phylostratum class
# # in two separate plots (groups)
# PlotMeans( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(group_1 = 1:3, group_2 = 4:12),
# legendName = "PS")
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Using the age.apply() function to compute the mean expression levels
# # of all Phylostrata
# age.apply( ExpressionSet = PhyloExpressionSetExample,
# FUN = colMeans )
## ---- fig.height= 5, fig.width=7,eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean gene expression of each Phylostratum class
# # and draw an shaded area for the mid-module.
# PlotMeans( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(1:12),
# modules = list(1:2,3:5,6:7),
# legendName = "PS")
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(DivergenceExpressionSetExample)
# # Visualizing the mean gene expression of each Divergence Stratum class
# PlotMeans( ExpressionSet = DivergenceExpressionSetExample,
# Groups = list(1:10),
# legendName = "DS",
# xlab = "Ontogeny")
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Using the age.apply() function to compute the mean expression levels
# # of all Divergence Strata
# age.apply( ExpressionSet = DivergenceExpressionSetExample,
# FUN = colMeans )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean gene expression of each Phylostratum class
# PlotRE( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(1:12),
# legendName = "PS",
# xlab = "Ontogeny")
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(DivergenceExpressionSetExample)
# # Visualizing the mean gene expression of each Divergence Stratum class
# PlotRE( ExpressionSet = DivergenceExpressionSetExample,
# Groups = list(1:10),
# legendName = "DS",
# xlab = "Ontogeny")
## ----fig.height=5, fig.width=7,eval=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean gene expression of each Phylostratum class
# PlotRE( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(group_1 = 1:3, group_2 = 4:12),
# legendName = "PS",
# xlab = "Ontogeny")
## ----fig.height=5, fig.width=7,eval=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean gene expression of each Phylostratum class
# PlotRE( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(1:12),
# modules = list(1:2,3:5,6:7),
# legendName = "PS",
# xlab = "Ontogeny")
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Getting the relative expression levels for all Phylostrata
# REMatrix(PhyloExpressionSetExample)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Getting the relative expression levels for all Divergence-Strata
# REMatrix(DivergenceExpressionSetExample)
## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Getting the relative expression levels for all Phylostrata
# age.apply( ExpressionSet = PhyloExpressionSetExample,
# FUN = RE )
## ----fig.height=5, fig.width=7,eval=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean relative expression of two Phylostratum groups
# PlotBarRE( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(group_1 = 1:3, group_2 = 4:12),
# xlab = "Ontogeny",
# ylab = "Mean Relative Expression",
# cex = 1.5)
## ---- fig.height=5,fig.width=7,eval=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean relative expression of two Phylostratum groups
# PlotBarRE( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(group_1 = 1:3, group_2 = 4:12),
# ratio = TRUE,
# xlab = "Ontogeny",
# ylab = "Mean Relative Expression",
# cex = 1.5 )
## ---- fig.width=7,eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Visualizing the mean relative expression of three Phylostratum groups
# PlotBarRE( ExpressionSet = PhyloExpressionSetExample,
# Groups = list(group_1 = 1:3, group_2 = 4:6, group_3 = 7:12),
# wLength = 0.05,
# xlab = "Ontogeny",
# ylab = "Mean Relative Expression",
# cex = 1.5 )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Display the phylostratum distribution (gene frequency distribution)
# # of a PhyloExpressionSet as absolute frequency distribution
# PlotDistribution( PhyloExpressionSet = PhyloExpressionSetExample,
# xlab = "Phylostratum" )
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # Plot phylostrata as relative frequency distribution
# PlotDistribution( PhyloExpressionSet = PhyloExpressionSetExample,
# as.ratio = TRUE,
# xlab = "Phylostratum")
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#
# # save the TAI profile to a local machine with png()
# png("ExampleTAIProfile.png", width = 800, height = 600)
#
# PlotPattern( ExpressionSet = PhyloExpressionSetExample,
# type = "l",
# lwd = 6,
# xlab = "Ontogeny",
# ylab = "TAI",
# cex = 1,
# cex.lab = 1,
# cex.axis = 1.2 )
#
# dev.off()
## ---- fig.width= 7, fig.height= 5,eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# # store ggplot2 graphic in variable p
# p <- PlotSignature(ExpressionSet = PhyloExpressionSetExample,
# ylab = "Transcriptome Age Index")
#
# # save ggplot2 based TAI profile to a local machine with save_plot()
# cowplot::save_plot("ExampleTAIProfile.pdf",
# p,
# base_height = 8,
# base_width = 12 )
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