## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", error = FALSE, warning = FALSE, message = FALSE, crop = NULL ) stopifnot(requireNamespace("htmltools")) htmltools::tagList(rmarkdown::html_dependency_font_awesome()) sce <- readRDS('sce.rds') ## ----------------------------------------------------------------------------- # Coloring for log-counts: logcounts_color_fun <- viridis::viridis ## ----------------------------------------------------------------------------- # Coloring for FPKMs: fpkm_color_fun <- function(n){ c("black","brown","red","orange","yellow") } ## ----driver_color_fun--------------------------------------------------------- # Coloring for the 'driver' metadata variable. driver_color_fun <- function(n){ RColorBrewer::brewer.pal(n, "Set2") } ## ----qc_color_fun------------------------------------------------------------- # Coloring for the QC metadata variable: qc_color_fun <- function(n){ qc_colors <- c("forestgreen", "firebrick1") names(qc_colors) <- c("Y", "N") qc_colors } ## ----ecm---------------------------------------------------------------------- library(iSEE) ecm <- ExperimentColorMap( assays = list( counts = heat.colors, logcounts = logcounts_color_fun, cufflinks_fpkm = fpkm_color_fun ), colData = list( passes_qc_checks_s = qc_color_fun, driver_1_s = driver_color_fun ), all_continuous = list( assays = viridis::plasma ) ) ecm ## ----all_continuous----------------------------------------------------------- ExperimentColorMap( all_continuous=list( # shared assays=viridis::plasma, colData=viridis::inferno ), global_continuous=viridis::magma # global ) ## ----allen-dataset-4---------------------------------------------------------- app <- iSEE(sce, colormap = ecm) ## ----runApp, eval=FALSE------------------------------------------------------- # shiny::runApp(app) ## ----sessioninfo-------------------------------------------------------------- sessionInfo() # devtools::session_info()