## ----setup, eval=TRUE, include=FALSE------------------------------------------ library(epivizrChart) library(antiProfilesData) library(SummarizedExperiment) library(RColorBrewer) library(Homo.sapiens) library(AnnotationHub) library(GenomicRanges) ## ----------------------------------------------------------------------------- data(tcga_colon_blocks) data(tcga_colon_curves) data(tcga_colon_expression) data(apColonData) ## ----------------------------------------------------------------------------- library(Homo.sapiens) genes_track <- epivizChart(Homo.sapiens, chr="chr11", start=118000000, end=121000000) genes_track ## ----------------------------------------------------------------------------- scatter_plot <- epivizChart(tcga_colon_curves, chr="chr11", start=99800000, end=103383180, type="bp", columns=c("cancerMean","normalMean"), chart="ScatterPlot") scatter_plot ## ----------------------------------------------------------------------------- epivizEnv <- epivizEnv(chr="chr11", start=118000000, end=121000000) genes_track <- epivizEnv$plot(Homo.sapiens) blocks_track <- epivizEnv$plot(tcga_colon_blocks, datasource_name="450kMeth") epivizEnv ## ----------------------------------------------------------------------------- epivizNav <- epivizNav(chr="chr11", start=118000000, end=121000000) genes_track <- epivizNav$plot(Homo.sapiens) blocks_track <- epivizNav$plot(tcga_colon_blocks, datasource_name="450kMeth") epivizNav ## ----------------------------------------------------------------------------- epivizEnv <- epivizEnv(chr="chr11", start=99800000, end=103383180) ## ----warning=FALSE, message=FALSE--------------------------------------------- require(Homo.sapiens) genes_track <- epivizEnv$plot(Homo.sapiens) genes_track ## ----------------------------------------------------------------------------- blocks_track <- epivizEnv$plot(tcga_colon_blocks, datasource_name="450kMeth") blocks_track ## ----eval=FALSE--------------------------------------------------------------- # epivizEnv ## ----------------------------------------------------------------------------- means_track <- epivizEnv$plot(tcga_colon_curves, datasource_name="450kMeth", type="bp", columns=c("cancerMean","normalMean")) means_track ## ----warning=FALSE, message=FALSE--------------------------------------------- keep <- pData(apColonData)$SubType!="adenoma" apColonData <- apColonData[,keep] status <- pData(apColonData)$Status Indexes <- split(seq(along=status),status) exprMat <- exprs(apColonData) mns <- sapply(Indexes, function(ind) rowMeans(exprMat[,ind])) mat <- cbind(colonM=mns[,"1"]-mns[,"0"], colonA=0.5*(mns[,"1"]+mns[,"0"])) pd <- data.frame(stat=c("M","A")) rownames(pd) <- colnames(mat) maEset <- ExpressionSet( assayData=mat, phenoData=AnnotatedDataFrame(pd), featureData=featureData(apColonData), annotation=annotation(apColonData) ) eset_chart <- epivizEnv$plot(maEset, datasource_name="MAPlot", columns=c("colonA","colonM")) eset_chart ## ----------------------------------------------------------------------------- ref_sample <- 2 ^ rowMeans(log2(assay(tcga_colon_expression) + 1)) scaled <- (assay(tcga_colon_expression) + 1) / ref_sample scaleFactor <- Biobase::rowMedians(t(scaled)) assay_normalized <- sweep(assay(tcga_colon_expression), 2, scaleFactor, "/") assay(tcga_colon_expression) <- assay_normalized status <- colData(tcga_colon_expression)$sample_type index <- split(seq(along = status), status) logCounts <- log2(assay(tcga_colon_expression) + 1) means <- sapply(index, function(ind) rowMeans(logCounts[, ind])) mat <- cbind(cancer = means[, "Primary Tumor"], normal = means[, "Solid Tissue Normal"]) sumexp <- SummarizedExperiment(mat, rowRanges=rowRanges(tcga_colon_expression)) se_chart <- epivizEnv$plot(sumexp, datasource_name="Mean by Sample Type", columns=c("normal", "cancer")) se_chart ## ----------------------------------------------------------------------------- # get measurements measurements <- se_chart$get_measurements() # create a heatmap using these measurements heatmap_plot <- epivizEnv$plot(measurements=measurements, chart="HeatmapPlot") heatmap_plot ## ----eval=FALSE--------------------------------------------------------------- # order <- list( # heatmap_plot, # genes_track, # blocks_track, # means_track, # se_chart, # eset_chart # ) # # epivizEnv$order_charts(order) ## ----------------------------------------------------------------------------- epivizEnv ## ----eval=FALSE--------------------------------------------------------------- # epivizEnv$navigate(chr="chr11", start=110800000, end=130383180) # epivizEnv ## ----eval=FALSE--------------------------------------------------------------- # # create an environment to show data from entire chromosome 11 # epivizEnv <- epivizEnv(chr="chr11") # # # add a line track from tcga_colon_curves object to the environment # means_track <- epivizEnv$plot(tcga_colon_curves, datasource_name="450kMeth", type="bp", columns=c("cancerMean","normalMean")) # # # add a scatter plot from the summarized experiment object to the environment # se_chart <- epivizEnv$plot(sumexp, datasource_name="Mean by Sample Type", columns=c("normal", "cancer")) # # # create a new navigation element that shows a particular region in chr11 # epivizNav <- epivizNav(chr="chr11", start=99800000, end=103383180, parent=epivizEnv) # # # add a blocks track to the navigation element # blocks_track <- epivizNav$plot(tcga_colon_blocks, datasource_name="450kMeth") # # epivizEnv ## ----eval=FALSE--------------------------------------------------------------- # epivizEnv <- epivizEnv(chr="chr11") # # # add a blocks track to the evironment # blocks_track <- epivizEnv$plot(tcga_colon_blocks, datasource_name="450kMeth") # # add a scatter plot from the summarized experiment object to the environment # se_chart <- epivizEnv$plot(sumexp, datasource_name="Mean by Sample Type", columns=c("normal", "cancer")) # # epivizNav <- epivizEnv$init_region(chr="chr11", start=99800000, end=103383180) # # epivizEnv ## ----eval=FALSE--------------------------------------------------------------- # epivizEnv$remove_all_charts() ## ----eval=FALSE--------------------------------------------------------------- # colors <- brewer.pal(3, "Dark2") # # blocks_track <- epivizChart(tcga_colon_blocks, chr="chr11", start=99800000, end=103383180, colors=colors) # # # to list availble settings for a chart # blocks_track$get_available_settings() # # settings <- list( # title="Blocks", # minBlockDistance=10 # ) # # blocks_track$set_settings(settings) # blocks_track # # blocks_track$set_colors(c("#D95F02")) # blocks_track # # colors <- brewer.pal(3, "Dark2") # lines_track <- epivizChart(tcga_colon_curves, chr="chr11", start=99800000, end=103383180, type="bp", columns=c("cancerMean","normalMean")) # lines_track # # lines_track$set_colors(colors) # lines_track ## ----eval=FALSE--------------------------------------------------------------- # # library(epivizrChart) # # # initialize environment with interactive = true. this argument will init. an epiviz-data-source element # epivizEnv <- epivizEnv(chr="chr11", start=118000000, end=121000000, interactive=TRUE) # ## ----eval=FALSE--------------------------------------------------------------- # library(epivizrServer) # # library(Homo.sapiens) # data(tcga_colon_blocks) # # # initialize server # server <- epivizrServer::createServer() # # # register all our actions between websocket and components # epivizrChart:::.register_all_the_epiviz_things(server, epivizEnv) # # # start server # server$start_server() ## ----eval=FALSE--------------------------------------------------------------- # # plot charts # blocks_track <- epivizEnv$plot(tcga_colon_blocks, datasource_name="450kMeth") # epivizEnv # # genes <- epivizEnv$plot(Homo.sapiens) # epivizEnv ## ----eval=FALSE--------------------------------------------------------------- # server$stop_server() ## ----------------------------------------------------------------------------- ah <- AnnotationHub() epi <- query(ah, c("roadmap")) df <- epi[["AH49015"]] ## ----------------------------------------------------------------------------- rna_plot <- epivizChart(df, datasource_name="RNASeq", columns=c("E006","E114"), chart="ScatterPlot") rna_plot