## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) stopifnot(requireNamespace("htmltools")) htmltools::tagList(rmarkdown::html_dependency_font_awesome()) ## ----setup-------------------------------------------------------------------- library(ExploreModelMatrix) ## ----fig.width = 5------------------------------------------------------------ (sampleData <- data.frame(genotype = rep(c("A", "B"), each = 4), treatment = rep(c("ctrl", "trt"), 4))) vd <- VisualizeDesign(sampleData = sampleData, designFormula = ~ genotype + treatment, textSizeFitted = 4) cowplot::plot_grid(plotlist = vd$plotlist) app <- ExploreModelMatrix(sampleData = sampleData, designFormula = ~ genotype + treatment) if (interactive()) { shiny::runApp(app) } ## ----fig.width = 5, fig.height = 12------------------------------------------- (sampleData <- data.frame( Response = rep(c("Resistant", "Sensitive"), c(12, 18)), Patient = factor(rep(c(1:6, 8, 11:18), each = 2)), Treatment = factor(rep(c("pre","post"), 15)), ind.n = factor(rep(c(1:6, 2, 5:12), each = 2)))) vd <- VisualizeDesign( sampleData = sampleData, designFormula = ~ Response + Response:ind.n + Response:Treatment, textSizeFitted = 3 ) cowplot::plot_grid(plotlist = vd$plotlist, ncol = 1) app <- ExploreModelMatrix( sampleData = sampleData, designFormula = ~ Response + Response:ind.n + Response:Treatment ) if (interactive()) { shiny::runApp(app) } ## ----fig.width = 5------------------------------------------------------------ vd <- VisualizeDesign(sampleData = sampleData, designFormula = ~ Treatment + Response, textSizeFitted = 4) cowplot::plot_grid(plotlist = vd$plotlist, ncol = 1) ## ----fig.height = 4, fig.width = 6-------------------------------------------- (sampleData = data.frame( condition = factor(rep(c("ctrl_minus", "ctrl_plus", "ko_minus", "ko_plus"), 3)), batch = factor(rep(1:6, each = 2)))) vd <- VisualizeDesign(sampleData = sampleData, designFormula = ~ 0 + batch + condition, textSizeFitted = 4, lineWidthFitted = 20, dropCols = "conditionko_minus") cowplot::plot_grid(plotlist = vd$plotlist, ncol = 1) app <- ExploreModelMatrix(sampleData = sampleData, designFormula = ~ batch + condition) if (interactive()) { shiny::runApp(app) } ## ----------------------------------------------------------------------------- if (interactive()) { out <- shiny::runApp(app) } ## ----------------------------------------------------------------------------- sessionInfo()