## ----setup, include=F,eval=T,echo=F--------------------------------------
knitr::opts_chunk$set(cache = TRUE,eval=F,echo = T)
file.type='html'
## ----results='asis',echo=F,eval=TRUE-------------------------------------
if(file.type=='html')
cat('<img src="fig/figures_001.png" width="900px />')
if(file.type=='word')
cat('![](fig/figures_001.png)')
if(file.type=='readme')
cat('![](https://github.com/wyguo/TSIS/blob/master/vignettes/fig/figures_001.png)')
## ------------------------------------------------------------------------
# R.home()
## ------------------------------------------------------------------------
# library(devtools)
# devtools::install_github("wyguo/TSIS")
## ------------------------------------------------------------------------
# library(TSIS)
## ------------------------------------------------------------------------
# TSIS.data.example()
## ------------------------------------------------------------------------
# TSIS.app(data.size.max = 100)
## ----results='asis',echo=F,eval=TRUE-------------------------------------
if(file.type=='html')
cat('<img src="fig/figures_002.png" width="900px" />')
if(file.type=='word')
cat('![](fig/figures_002.png)')
if(file.type=='readme')
cat('![](https://github.com/wyguo/TSIS/blob/master/vignettes/fig/figures_002.png)')
## ----results='asis',echo=F,eval=TRUE-------------------------------------
if(file.type=='html')
cat('<img src="fig/figures_003.png" width="900px" />')
if(file.type=='word')
cat('![](fig/figures_003.png)')
if(file.type=='readme')
cat('![](https://github.com/wyguo/TSIS/blob/master/vignettes/fig/figures_003.png)')
## ----results='asis',echo=F,eval=TRUE-------------------------------------
if(file.type=='html')
cat('<img src="fig/figures_004.png" width="900px" />')
if(file.type=='word')
cat('![](fig/figures_004.png)')
if(file.type=='readme')
cat('![](https://github.com/wyguo/TSIS/blob/master/vignettes/fig/figures_004.png)')
## ----results='asis',echo=F,eval=TRUE-------------------------------------
if(file.type=='html')
cat('<img src="fig/figures_005.png" width="900px" />')
if(file.type=='word')
cat('![](fig/figures_005.png)')
if(file.type=='readme')
cat('![](https://github.com/wyguo/TSIS/blob/master/vignettes/fig/figures_005.png)')
## ----results='asis',echo=F,eval=TRUE-------------------------------------
if(file.type=='html')
cat('<img src="fig/figures_006.png" width="900px" />')
if(file.type=='word')
cat('![](fig/figures_006.png)')
if(file.type=='readme')
cat('![](https://github.com/wyguo/TSIS/blob/master/vignettes/fig/figures_006.png)')
## ----results='asis',echo=F,eval=TRUE-------------------------------------
if(file.type=='html')
cat('<img src="fig/figures_007.png" width="900px" />')
if(file.type=='word')
cat('![](fig/figures_007.png)')
if(file.type=='readme')
cat('![](https://github.com/wyguo/TSIS/blob/master/vignettes/fig/figures_007.png)')
## ----results='asis',echo=F,eval=TRUE-------------------------------------
if(file.type=='html')
cat('<img src="fig/figures_008.png" width="900px" />')
if(file.type=='word')
cat('![](fig/figures_008.png)')
if(file.type=='readme')
cat('![](https://github.com/wyguo/TSIS/blob/master/vignettes/fig/figures_008.png)')
## ----eval=F,echo=T-------------------------------------------------------
# ##load the data
# library(TSIS)
# data.exp<-TSIS.data$data.exp
# mapping<-TSIS.data$mapping
# dim(data.exp);dim(mapping)
## ----echo=T,eval=F-------------------------------------------------------
# ##Scores
# scores.mean2int<-iso.switch(data.exp=data.exp,mapping =mapping,
# times=rep(1:26,each=9),rank=F,
# min.t.points =2,min.difference=1,spline =F,
# spline.df = 9,verbose = F)
## ------------------------------------------------------------------------
# ##Scores, set spline=T and define spline degree of freedom to spline.df=9
# scores.spline2int<-iso.switch(data.exp=data.exp,mapping =mapping,
# times=rep(1:26,each=9),rank=F,
# min.t.points =2,min.difference=1,spline =T,
# spline.df = 10,verbose = F)
## ----eval=F--------------------------------------------------------------
# ##intersection from mean expression
# scores.mean2int.filtered<-score.filter(
# scores = scores.mean2int,prob.cutoff = 0.5,diff.cutoff = 1,
# t.points.cutoff = 2,pval.cutoff = 0.001, cor.cutoff = 0,
# data.exp = NULL,mapping = NULL,sub.isoform.list = NULL,
# sub.isoform = F,max.ratio = F,x.value.limit = c(1,26)
# )
# scores.mean2int.filtered[1:5,]
## ------------------------------------------------------------------------
# ##intersection from spline method
# scores.spline2int.filtered<-score.filter(
# scores = scores.spline2int,prob.cutoff = 0.5,
# diff.cutoff = 1,t.points.cutoff = 2,pval.cutoff = 0.01,
# cor.cutoff = 0.5,data.exp = NULL,mapping = NULL,
# sub.isoform.list = NULL,sub.isoform = F,max.ratio = F,
# x.value.limit = c(9,17)
# ))
## ------------------------------------------------------------------------
# ##intersection from mean expression
# ##input a list of isoform names for investigation.
# sub.isoform.list<-TSIS.data$sub.isoforms
# sub.isoform.list[1:10]
# ##assign the isoform name list to sub.isoform.list and set sub.isoform=TRUE
# scores.mean2int.filtered.subset<-score.filter(
# scores = scores.mean2int,prob.cutoff = 0.5,diff.cutoff = 1,
# t.points.cutoff = 2,pval.cutoff = 0.01, cor.cutoff = 0.5,
# data.exp = NULL,mapping = NULL,sub.isoform.list = sub.isoform.list,
# sub.isoform = T,max.ratio = F,x.value.limit = c(9,17)
# )
## ------------------------------------------------------------------------
# scores.mean2int.filtered.maxratio<-score.filter(
# scores = scores.mean2int,prob.cutoff = 0.5,diff.cutoff = 1,
# t.points.cutoff = 2,pval.cutoff = 0.01, cor.cutoff = 0,
# data.exp = data.exp,mapping = mapping,sub.isoform.list = NULL,
# sub.isoform = F,max.ratio = T,x.value.limit = c(9,17)
# )
## ------------------------------------------------------------------------
# library(gridExtra)
# g1<-switch.density(scores.mean2int.filtered$x.value,make.plotly = F,
# show.line = F,plot.type = 'frequency',
# title = 'Frequency of switch time' ,time.points = 1:26)
# g2<-switch.density(scores.mean2int.filtered$x.value,make.plotly = F,
# show.line = T,plot.type = 'density',
# title = 'Density of switch time' ,time.points = 1:26)
# gridExtra::grid.arrange(g1,g2,ncol=2)
## ----results='asis',echo=F,eval=TRUE-------------------------------------
if(file.type=='html')
cat('<img src="fig/figures_009.png" width="900px" />')
if(file.type=='word')
cat('![](fig/figures_009.png)')
if(file.type=='readme')
cat('![](https://github.com/wyguo/TSIS/blob/master/vignettes/fig/figures_009.png)')
## ------------------------------------------------------------------------
# plotTSIS(data2plot = data.exp,scores = scores.mean2int.filtered,
# iso1 = 'G30.iso2',iso2 = 'G30.iso3',gene.name = NULL,
# y.lab = 'Expression',make.plotly = F,
# times=rep(1:26,each=9),prob.cutoff = 0.5,
# x.lower.boundary = 9,x.upper.boundary = 17,
# show.region = T,show.scores = T,
# line.width =0.5,point.size = 3,
# error.type = 'stderr',show.errorbar = T,errorbar.size = 0.5,
# errorbar.width = 0.2,spline = F,spline.df = NULL,ribbon.plot = F)
## ----results='asis',echo=F,eval=TRUE-------------------------------------
if(file.type=='html')
cat('<img src="fig/figures_010.png" width="900px" />')
if(file.type=='word')
cat('![](fig/figures_010.png)')
if(file.type=='readme')
cat('![](https://github.com/wyguo/TSIS/blob/master/vignettes/fig/figures_010.png)')
## ------------------------------------------------------------------------
# plotTSIS(data2plot = data.exp,scores = scores.mean2int.filtered,
# iso1 = 'G30.iso2',iso2 = 'G30.iso3',gene.name = NULL,
# y.lab = 'Expression',make.plotly = F,
# times=rep(1:26,each=9),prob.cutoff = 0.5,
# x.lower.boundary = 9,x.upper.boundary = 17,
# show.region = T,show.scores = T,
# line.width =0.5,point.size = 3,
# error.type = 'stderr',show.errorbar = T,errorbar.size = 0.5,
# errorbar.width = 0.2,spline = F,spline.df = NULL,ribbon.plot = T)
## ----results='asis',echo=F,eval=TRUE-------------------------------------
if(file.type=='html')
cat('<img src="fig/figures_011.png" width="900px" />')
if(file.type=='word')
cat('![](fig/figures_011.png)')
if(file.type=='readme')
cat('![](https://github.com/wyguo/TSIS/blob/master/vignettes/fig/figures_010.png)')
## ----results='asis',echo=F,eval=TRUE-------------------------------------
if(file.type!='readme')
cat('#Session Information')
## ----session, echo=FALSE,eval=T------------------------------------------
if(file.type!='readme')
sessionInfo()
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