## ----setup, eval=TRUE, include=FALSE---------------------------------------
library(epivizrChart)
library(antiProfilesData)
library(SummarizedExperiment)
library(RColorBrewer)
library(Homo.sapiens)

## --------------------------------------------------------------------------
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

## --------------------------------------------------------------------------
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

## --------------------------------------------------------------------------
order <- list(
  heatmap_plot,
  genes_track,
  blocks_track,
  means_track,
  se_chart,
  eset_chart
)

epivizEnv$order_charts(order)

## --------------------------------------------------------------------------
epivizEnv

## --------------------------------------------------------------------------
epivizEnv$navigate(chr="chr11", start=110800000, end=130383180)
epivizEnv

## --------------------------------------------------------------------------
# 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

## --------------------------------------------------------------------------
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

## --------------------------------------------------------------------------
epivizEnv$remove_all_charts()

## --------------------------------------------------------------------------
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()