Nothing
## ---- 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")
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