context("addCharts")
sendRequest <- getOption("epivizrTestSendRequest")
standalone <- getOption("epivizrTestStandalone")
test_that("blockChart works", {
sendRequest=sendRequest
gr <- GRanges(seqnames="chr1", ranges=IRanges(start=1:10, width=1))
mgr <- .startMGR(openBrowser=sendRequest)
tryCatch({
if (sendRequest) wait_until(mgr$server$socketConnected)
msObj <- mgr$addMeasurements(gr, "ms1", sendRequest=sendRequest)
msId <- msObj$getId()
if (sendRequest) wait_until(!mgr$server$requestWaiting)
if (standalone) {
mgr$addSeqinfo(seqinfo(gr))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
navigate_range <- gr[1,] + 2000
mgr$navigate(as.character(seqnames(navigate_range)), start(navigate_range), end(navigate_range))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
}
ms <- msObj$getMeasurements()
chartObj <- mgr$blockChart(ms, sendRequest=sendRequest)
chartId <- chartObj$getId()
if (sendRequest) wait_until(!mgr$server$requestWaiting)
expect_is(chartObj, "EpivizChart")
expect_equal(chartObj$measurements, ms)
expect_equal(chartObj$type, "epiviz.plugins.charts.BlocksTrack")
expect_false(is.null(mgr$chartList[[chartId]]))
connected <- !is.null(mgr$chartIdMap[[chartId]])
expect_equal(connected, sendRequest)
}, finally=mgr$stopServer())
})
test_that("plot block works", {
sendRequest=sendRequest
gr <- GRanges(seqnames="chr1", ranges=IRanges(start=1:10, width=1))
mgr <- .startMGR(openBrowser=sendRequest)
tryCatch({
if (sendRequest) wait_until(mgr$server$socketConnected)
msObj <- mgr$addMeasurements(gr, "ms1", sendRequest=sendRequest)
msId <- msObj$getId()
if (sendRequest) wait_until(!mgr$server$requestWaiting)
if (standalone) {
mgr$addSeqinfo(seqinfo(gr))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
navigate_range <- gr[1,] + 2000
mgr$navigate(as.character(seqnames(navigate_range)), start(navigate_range), end(navigate_range))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
}
chartObj <- msObj$plot(sendRequest=sendRequest)
chartId <- chartObj$getId()
# ms <- structure(msObj$getName(), names=msId)
ms <- msObj$getMeasurements()
expect_is(chartObj, "EpivizChart")
expect_equal(chartObj$measurements, ms)
expect_equal(chartObj$type, "epiviz.plugins.charts.BlocksTrack")
expect_false(is.null(mgr$chartList[[chartId]]))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
connected <- !is.null(mgr$chartIdMap[[chartId]])
expect_equal(connected, sendRequest)
}, finally=mgr$stopServer())
})
test_that("lineChart works", {
sendRequest=sendRequest
gr <- GRanges(seqnames="chr1", ranges=IRanges(start=seq(1,100,by=25), width=1),
score1=rnorm(length(seq(1,100,by=25))),score2=rnorm(length(seq(1,100,by=25))))
seqlengths(gr) <- c("chr1"=200000)
mgr <- .startMGR(openBrowser=sendRequest)
tryCatch({
if (sendRequest) wait_until(mgr$server$socketConnected)
msObj <- mgr$addMeasurements(gr, "ms1", sendRequest=sendRequest, type="bp")
msId <- msObj$getId()
if (sendRequest) wait_until(!mgr$server$requestWaiting)
# ms <- structure(paste0(msObj$getName(), "__score2"), names=paste0(msId,"__score2"))
if (standalone) {
mgr$addSeqinfo(seqinfo(gr))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
navigate_range <- gr[1,] + 2000
mgr$navigate(as.character(seqnames(navigate_range)), start(navigate_range), end(navigate_range))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
}
ms <- msObj$getMeasurements()[2]
chartObj <- mgr$lineChart(ms, sendRequest=sendRequest)
chartId <- chartObj$getId()
expect_equal(chartObj$measurements, ms)
expect_equal(chartObj$type, "epiviz.plugins.charts.LineTrack")
expect_false(is.null(mgr$chartList[[chartId]]))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
connected <- !is.null(mgr$chartIdMap[[chartId]])
expect_equal(connected, sendRequest)
}, finally=mgr$stopServer())
})
test_that("plot bp works", {
sendRequest=sendRequest
gr <- GRanges(seqnames="chr1", ranges=IRanges(start=seq(1,100,by=25), width=1),
score1=rnorm(length(seq(1,100,by=25))),score2=rnorm(length(seq(1,100,by=25))))
mgr <- .startMGR(openBrowser=sendRequest)
tryCatch({
if (sendRequest) wait_until(mgr$server$socketConnected)
msObj <- mgr$addMeasurements(gr, "ms1", sendRequest=sendRequest, type="bp")
msId <- msObj$getId()
if (standalone) {
mgr$addSeqinfo(seqinfo(gr))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
navigate_range <- gr[1,] + 2000
mgr$navigate(as.character(seqnames(navigate_range)), start(navigate_range), end(navigate_range))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
}
if (sendRequest) wait_until(!mgr$server$requestWaiting)
chartObj <- msObj$plot(sendRequest=sendRequest)
chartId <- chartObj$getId()
ms <- structure(paste0(msObj$getName(), "$score", 1:2), names=paste0(msId,"__score",1:2))
ms <- msObj$getMeasurements()
expect_equal(chartObj$measurements, ms)
expect_equal(chartObj$type, "epiviz.plugins.charts.LineTrack")
expect_false(is.null(mgr$chartList[[chartId]]))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
connected <- !is.null(mgr$chartIdMap[[chartId]])
expect_equal(connected, sendRequest)
}, finally=mgr$stopServer())
})
test_that("scatterChart works", {
sendRequest=sendRequest
sset <- makeSExp()
mgr <- .startMGR(openBrowser=sendRequest)
tryCatch({
if (sendRequest) wait_until(mgr$server$socketConnected)
msObj <- mgr$addMeasurements(sset, "ms1", sendRequest=sendRequest, columns=c("A","B"), assay="counts2")
msId <- msObj$getId()
if (sendRequest) wait_until(!mgr$server$requestWaiting)
if (standalone) {
mgr$addSeqinfo(seqinfo(sset))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
navigate_range <- rowData(sset)[1,] + 2000
mgr$navigate(as.character(seqnames(navigate_range)), start(navigate_range), end(navigate_range))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
}
x <- structure(paste0(msObj$getName(), "$A"), names=paste0(msId, "__A"))
y <- structure(paste0(msObj$getName(), "$B"), names=paste0(msId, "__B"))
ms <- msObj$getMeasurements()
chartObj <- mgr$scatterChart(x=ms[[1]], y=ms[[2]],sendRequest=sendRequest)
chartId <- chartObj$getId()
expect_equal(chartObj$measurements, ms)
expect_equal(chartObj$type, "epiviz.plugins.charts.ScatterPlot")
expect_false(is.null(mgr$chartList[[chartId]]))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
connected <- !is.null(mgr$chartIdMap[[chartId]])
expect_equal(connected, sendRequest)
}, finally=mgr$stopServer())
})
test_that("plot feature works", {
sendRequest=sendRequest
sset <- makeSExp()
mgr <- .startMGR(openBrowser=sendRequest)
tryCatch({
if (sendRequest) wait_until(mgr$server$socketConnected)
msObj <- mgr$addMeasurements(sset, "ms1", sendRequest=sendRequest, columns=c("A","B"), assay="counts2")
msId <- msObj$getId()
if (sendRequest) wait_until(!mgr$server$requestWaiting)
chartObj <- msObj$plot(sendRequest=sendRequest)
chartId <- chartObj$getId()
if (standalone) {
mgr$addSeqinfo(seqinfo(sset))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
navigate_range <- rowData(sset)[1,] + 2000
mgr$navigate(as.character(seqnames(navigate_range)), start(navigate_range), end(navigate_range))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
}
ms <- structure(paste0(msObj$getName(), "$", c("A","B")), names=paste0(msId, "__", c("A","B")))
ms <- msObj$getMeasurements()
# print(chartObj$measurements);print(ms)
expect_equal(chartObj$measurements, ms)
expect_equal(chartObj$type, "epiviz.plugins.charts.ScatterPlot")
expect_false(is.null(mgr$chartList[[chartId]]))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
connected <- !is.null(mgr$chartIdMap[[chartId]])
expect_equal(connected, sendRequest)
}, finally=mgr$stopServer())
})
test_that("plot gene track works", {
sendRequest=sendRequest
gr <- makeGeneInfo()
mgr <- .startMGR(openBrowser=sendRequest)
tryCatch({
if (sendRequest) wait_until(mgr$server$socketConnected)
msObj <- mgr$addMeasurements(gr, "hg19", type="geneInfo", sendRequest=sendRequest)
msId <- msObj$getId()
if (standalone) {
mgr$addSeqinfo(seqinfo(gr))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
navigate_range <- gr[1,] + 2000
mgr$navigate(as.character(seqnames(navigate_range)), start(navigate_range), end(navigate_range))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
}
if (sendRequest) wait_until(!mgr$server$requestWaiting)
chartObj <- msObj$plot(sendRequest=sendRequest)
chartId <- chartObj$getId()
ms <- msObj$getMeasurements()
expect_equal(chartObj$measurements, ms)
expect_equal(chartObj$type, "epiviz.plugins.charts.GenesTrack")
expect_false(is.null(mgr$chartList[[chartId]]))
if (sendRequest) wait_until(!mgr$server$requestWaiting)
connected <- !is.null(mgr$chartIdMap[[chartId]])
expect_equal(connected, sendRequest)
}, finally=mgr$stopServer())
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.