## ----knitr, echo=FALSE, results='hide'------------------------------------------------------------ library("knitr") opts_chunk$set(tidy=FALSE,dev="png",fig.show="show", # fig.width=7,fig.height=7, echo=TRUE, message=FALSE, warning=FALSE) ## ----initialize, cache=FALSE, echo=FALSE---------------------------------------------------------- # load library library('variancePartition') ## ----corStruct, results='hide'-------------------------------------------------------------------- # Fit linear mixed model and examine correlation stucture # for one gene data(varPartData) form <- ~ Age + (1|Individual) + (1|Tissue) fitList <- fitVarPartModel( geneExpr[1:2,], form, info ) # focus on one gene fit = fitList[[1]] ## ----corStructa,out.width = "50%"----------------------------------------------------------------- # Figure 1a # correlation structure based on similarity within Individual # reorder samples based on clustering plotCorrStructure( fit, "Individual" ) ## ----corStructb,out.width = "50%"----------------------------------------------------------------- # Figure 1b # use original order of samples plotCorrStructure( fit, "Individual", reorder=FALSE ) ## ----corStructc,out.width = "50%"----------------------------------------------------------------- # Figure 1c # correlation structure based on similarity within Tissue # reorder samples based on clustering plotCorrStructure( fit, "Tissue" ) ## ----corStructd,out.width = "50%"----------------------------------------------------------------- # Figure 1d # use original order of samples plotCorrStructure( fit, "Tissue", reorder=FALSE ) ## ----corStructe,out.width = "50%"----------------------------------------------------------------- # Figure 2a # correlation structure based on similarity within # Individual *and* Tissue, reorder samples based on clustering plotCorrStructure( fit ) ## ----corStructf,out.width = "50%"----------------------------------------------------------------- # Figure 2b # use original order of samples plotCorrStructure( fit, reorder=FALSE )