## ----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, fig.width=7, fig.height=7-------------------------------------------------------- # Figure 1a # correlation structure based on similarity within Individual # reorder samples based on clustering plotCorrStructure(fit, "Individual") ## ----corStructb, fig.width=7, fig.height=7-------------------------------------------------------- # Figure 1b # use original order of samples plotCorrStructure(fit, "Individual", reorder = FALSE) ## ----corStructc, fig.width=7, fig.height=7-------------------------------------------------------- # Figure 1c # correlation structure based on similarity within Tissue # reorder samples based on clustering plotCorrStructure(fit, "Tissue") ## ----corStructd, fig.width=7, fig.height=7-------------------------------------------------------- # Figure 1d # use original order of samples plotCorrStructure(fit, "Tissue", reorder = FALSE) ## ----corStructe, fig.width=7, fig.height=7-------------------------------------------------------- # Figure 2a # correlation structure based on similarity within # Individual *and* Tissue, reorder samples based on clustering plotCorrStructure(fit) ## ----corStructf, fig.width=7, fig.height=7-------------------------------------------------------- # Figure 2b # use original order of samples plotCorrStructure(fit, reorder = FALSE) ## ----session, echo=FALSE-------------------------------------------------------------------------- sessionInfo()