Advanced.R
In myTAI: Evolutionary Transcriptomics

## ---- echo = FALSE, message = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
library(myTAI)
options(width = 750)
knitr::opts_chunk$set(
  comment = "#>",
  error = FALSE,
  tidy = FALSE)

## ----eval = FALSE, fig.width= 7, fig.height= 5------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  library(myTAI)
#  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)

## ----eval = FALSE, fig.width= 7, fig.height= 5------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  library(myTAI)
#  data(PhyloExpressionSetExample)
#  # stage-centered visualization of PS specific expression level distributions (log-scale)
#  PlotCategoryExpr(ExpressionSet = PhyloExpressionSetExample,
#                   legendName    = "PS",
#                   test.stat     = TRUE,
#                   type          = "stage-centered",
#                   distr.type    = "boxplot",
#                   log.expr      = TRUE)

## ----eval = FALSE, fig.width= 7, fig.height= 5------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  data(PhyloExpressionSetExample)
#  # category-centered visualization of PS specific expression level distributions (log-scale)
#  PlotCategoryExpr(ExpressionSet = tf(PhyloExpressionSetExample, log2),
#                   legendName    = "PS",
#                   test.stat     = TRUE,
#                   type          = "category-centered",
#                   distr.type    = "boxplot",
#                   log.expr      = FALSE)

## ----eval = FALSE, fig.width= 7, fig.height= 5------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  data(PhyloExpressionSetExample)
#  # category-centered visualization of PS specific expression level distributions (sqrt-scale)
#  PlotCategoryExpr(ExpressionSet = tf(PhyloExpressionSetExample, sqrt),
#                   legendName    = "PS",
#                   test.stat     = TRUE,
#                   type          = "category-centered",
#                   distr.type    = "boxplot",
#                   log.expr      = FALSE)

## ----eval = FALSE, fig.width= 7, fig.height= 5------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  library(myTAI)
#  data(PhyloExpressionSetExample)
#  # define an example gene subset (500 genes) which
#  # can be found in the input ExpressionSet
#  set.seed(234)
#  example.gene.set <- PhyloExpressionSetExample[sample(1:25260,500) , 2]
#  # visualize the gene expression distributions for these 500 genes (category-centered)
#  PlotCategoryExpr(ExpressionSet = PhyloExpressionSetExample,
#                   legendName    = "PS",
#                   test.stat     = TRUE,
#                   type          = "category-centered",
#                   distr.type    = "boxplot",
#                   log.expr      = TRUE,
#                   gene.set      = example.gene.set)

## ----eval = FALSE, fig.width= 7, fig.height= 5------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  library(myTAI)
#  data(PhyloExpressionSetExample)
#  # define an example gene subset (500 genes) which
#  # can be found in the input ExpressionSet
#  set.seed(234)
#  example.gene.set <- PhyloExpressionSetExample[sample(1:25260,500) , 2]
#  # visualize the gene expression distributions for these 500 genes (stage-centered)
#  PlotCategoryExpr(ExpressionSet = PhyloExpressionSetExample,
#                   legendName    = "PS",
#                   test.stat     = TRUE,
#                   type          = "stage-centered",
#                   distr.type    = "boxplot",
#                   log.expr      = TRUE,
#                   gene.set      = example.gene.set)

## ----eval= FALSE, fig.width= 7, fig.height= 7,warning=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  library(myTAI)
#  data(PhyloExpressionSetExample)
#  
#  PlotGroupDiffs(ExpressionSet = PhyloExpressionSetExample,
#                 Groups        = list(group_1 = 1:3,group_2 = 4:12),
#                 legendName    = "PS",
#                 plot.type     = "p-vals",
#                 type          = "b",
#                 lwd           = 6,
#                 xlab          = "Ontogeny")

## ----eval= FALSE, fig.width= 9, fig.height= 7,warning=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  library(myTAI)
#  data(PhyloExpressionSetExample)
#  # only receive the p-values without the corresponding plot
#  PlotGroupDiffs(ExpressionSet = PhyloExpressionSetExample,
#                 Groups        = list(group_1 = 1:3,group_2 = 4:12),
#                 legendName    = "PS",
#                 plot.type     = NULL)

## ----eval= FALSE,fig.width= 9, fig.height= 12,warning=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  library(myTAI)
#  data(PhyloExpressionSetExample)
#  # visualize difference as boxplot
#  PlotGroupDiffs(ExpressionSet = tf(PhyloExpressionSetExample,log2),
#                 Groups        = list(group_1 = 1:3,group_2 = 4:12),
#                 legendName    = "PS",
#                 plot.type     = "boxplot")