## ----include=FALSE------------------------------------------------------------ library(knitr) opts_chunk$set(concordance=TRUE) ## ----install1, eval=FALSE, results='asis'------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("interactiveDisplay") ## ----install2, eval=FALSE, results='asis'------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install(version = "devel") # BiocManager::install("interactiveDisplay") ## ----citation, eval=TRUE, results='tex'--------------------------------------- citation("interactiveDisplay") ## ----libraries, eval=TRUE, results='asis'------------------------------------- options(width=80) options(continue=" ") suppressMessages(library(ggplot2)) suppressMessages(library(interactiveDisplay)) suppressMessages(library(Biobase)) ## ----data_mmgr, eval=TRUE, results='tex'-------------------------------------- data(mmgr) mmgr ## ----grl, eval=TRUE, results='tex'-------------------------------------------- grl <- GRangesList(list(mmgr,mmgr)) ## ----data_mmgrl, eval=TRUE, results='tex'------------------------------------- data(mmgrl) mmgrl ## ----display_mmgr, eval=FALSE, results='asis'--------------------------------- # display(mmgr) ## ----display_mmgrl, eval=FALSE, results='asis'-------------------------------- # display(mmgrl) ## ----display_mmgr2, eval=FALSE, results='asis'-------------------------------- # new_mmgr <- display(mmgr) ## ----display_mmgrl2, eval=FALSE, results='asis'------------------------------- # new_mmgrl <- display(mmgrl) ## ----data_expr, eval=TRUE, results='tex'-------------------------------------- data(expr) expr ## ----exprs_expr, eval=TRUE, results='tex'------------------------------------- exprs(expr)[1:10,1:7] ## ----display_expr, eval=FALSE, results='asis'--------------------------------- # display(expr) ## ----data_se, eval=TRUE, results='tex'---------------------------------------- data(se) se ## ----display_se, eval=FALSE, results='asis'----------------------------------- # display(se) ## ----display_mtcars, eval=FALSE, results='asis'------------------------------- # display(mtcars) ## ----display_mtcars2, eval=FALSE, results='asis'------------------------------ # new_mtcars <- display(mtcars) ## ----simplenet_mtcars, eval=FALSE, results='asis'----------------------------- # simplenet(mtcars) ## ----plot_mtcars, eval=FALSE, results='asis'---------------------------------- # data(mtcars) # qp <- qplot(mpg, data=mtcars, geom="density", fill=factor(cyl), alpha=I(.4)) # plot(qp) ## ----gridsvgjs_qp, eval=FALSE, results='asis'--------------------------------- # gridsvgjs(qp) ## ----sessionInfo, eval=TRUE, results='tex'------------------------------------ sessionInfo()