tests/testthat/test-map-markers.R
In VEuPathDB/plot.data: Create `data.table`s of Ready to Plot Data
context('mapMarkers')
test_that("mapMarkers.dt does not fail when there are no complete cases.", {
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'binary1', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
df <- data.noneComplete[is.na(entity.binary1),]
dt <- mapMarkers.dt(df, variables, value='count')
attr <- attributes(dt)
expect_equal(attr$completeCasesAllVars[1], 0)
expect_equal(is.list(dt$label), TRUE)
expect_equal(is.list(dt$value), TRUE)
dt <- mapMarkers.dt(df, variables, value='proportion')
attr <- attributes(dt)
expect_equal(attr$completeCasesAllVars[1], 0)
expect_equal(is.list(dt$label), TRUE)
expect_equal(is.list(dt$value), TRUE)
})
test_that("mapMarkers.dt() returns a valid plot.data mapMarkers object", {
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat4', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
df <- as.data.frame(testDF)
dt <- mapMarkers.dt(df, variables, value='count')
expect_is(dt, 'plot.data')
expect_is(dt, 'mapMarkers')
namedAttrList <- getPDAttributes(dt)
expect_equal(names(namedAttrList),c('variables', 'completeCasesAllVars','completeCasesAxesVars','completeCasesTable','sampleSizeTable','viewport'))
completeCases <- completeCasesTable(dt)
expect_equal(names(completeCases), c('variableDetails','completeCases'))
expect_equal(nrow(completeCases), 2)
sampleSizes <- sampleSizeTable(dt)
expect_equal(names(sampleSizes), c('entity.cat4','entity.cat6','size'))
expect_equal(nrow(sampleSizes), 4)
# Ensure sampleSizeTable and completeCasesTable do not get returned if we do not ask for them.
dt <- mapMarkers.dt(df, variables, value='count', sampleSizes = FALSE, completeCases = FALSE)
expect_is(dt, 'plot.data')
expect_is(dt, 'mapMarkers')
namedAttrList <- getPDAttributes(dt)
expect_equal(names(namedAttrList),c('variables','viewport'))
})
test_that("mapMarkers.dt() returns plot data and config of the appropriate types", {
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
df <- as.data.frame(testDF)
dt <- mapMarkers.dt(df, variables, value='count')
expect_is(dt$label, 'list')
expect_equal(class(unlist(dt$label)), 'character')
expect_is(dt$value, 'list')
expect_equal(class(unlist(dt$value)), 'integer')
namedAttrList <- getPDAttributes(dt)
expect_equal(class(namedAttrList$completeCasesAllVars),c('scalar', 'integer'))
expect_equal(class(namedAttrList$completeCasesAxesVars),c('scalar', 'integer'))
completeCases <- completeCasesTable(dt)
expect_equal(class(unlist(completeCases$variableDetails)), 'character')
expect_equal(class(unlist(completeCases$completeCases)), 'integer')
sampleSizes <- sampleSizeTable(dt)
expect_equal(class(unlist(sampleSizes$entity.cat5)), 'character')
expect_equal(class(unlist(sampleSizes$size)), 'integer')
})
test_that("mapMarkers.dt() returns an appropriately sized data.table", {
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat4', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
df <- as.data.frame(testDF)
dt <- mapMarkers.dt(df, variables, value='count')
expect_is(dt, 'data.table')
expect_is(dt, 'mapMarkers')
expect_equal(nrow(dt),4)
expect_equal(names(dt),c('entity.cat4', 'label', 'value'))
dt <- mapMarkers.dt(df, variables, value='proportion')
expect_is(dt, 'data.table')
expect_is(dt, 'mapMarkers')
expect_equal(nrow(dt),4)
expect_equal(names(dt),c('entity.cat4', 'label', 'value'))
expect_equal(all(grepl('.||.', dt$panel, fixed=T)), TRUE)
# sum of x counts within a group should sum to 1
expect_equal(all(lapply(dt$value, sum) == 1), TRUE)
# With factors
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'factor6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
dt <- mapMarkers.dt(df, variables, value='count')
expect_is(dt, 'data.table')
expect_is(dt, 'mapMarkers')
expect_equal(nrow(dt),6)
expect_equal(names(dt),c('entity.factor6', 'label', 'value'))
expect_equal(class(dt$entity.factor6), 'character')
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'factor6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
dt <- mapMarkers.dt(df, variables, value='count')
expect_is(dt, 'data.table')
expect_is(dt, 'mapMarkers')
expect_equal(nrow(dt),6)
expect_equal(names(dt),c('entity.factor6', 'label', 'value'))
expect_equal(class(dt$entity.factor6), 'character')
# With continuous x var (< 9 values)
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat4', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'NUMBER'),
dataShape = new("DataShape", value = 'CONTINUOUS'))
))
dt <- mapMarkers.dt(df, variables, value='count')
expect_is(dt, 'data.table')
expect_is(dt, 'mapMarkers')
expect_equal(nrow(dt),4)
expect_equal(names(dt),c('entity.cat4', 'label', 'value'))
dt <- mapMarkers.dt(df, variables, value='proportion')
expect_is(dt, 'data.table')
expect_is(dt, 'mapMarkers')
expect_equal(nrow(dt),4)
expect_equal(names(dt),c('entity.cat4', 'label', 'value'))
# sum of x counts within a group should sum to 1
expect_equal(all(lapply(dt$value, sum) == 1), TRUE)
})
test_that("mapMarkers() returns appropriately formatted json", {
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cont6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'longitude'),
dataType = new("DataType", value = 'LONGITUDE'),
dataShape = new("DataShape", value = 'CONTINUOUS')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cont5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'latitude'),
dataType = new("DataType", value = 'NUMBER'),
dataShape = new("DataShape", value = 'CONTINUOUS')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int7', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
df <- as.data.frame(testDF)
df$entity.int7 <- as.character(df$entity.int7)
viewport <- list('latitude'=list('xMin'=-.5,
'xMax'=.5),
'longitude'=list('left'=-.5,
'right'=.5))
dt <- mapMarkers.dt(df, variables, value='count', viewport=viewport)
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(class(unlist(jsonList$mapMarkers$config$viewport)), 'numeric')
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cont6','cont5','cat5','int7'))
expect_equal(names(jsonList$sampleSizeTable), c('geoAggregateVariableDetails','xVariableDetails','size'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(class(jsonList$sampleSizeTable$xVariableDetails$value[[1]]), 'character')
expect_equal(jsonList$sampleSizeTable$xVariableDetails$variableId[1], 'int7')
expect_equal(names(jsonList$completeCasesTable), c('variableDetails','completeCases'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId'))
expect_equal(jsonList$completeCasesTable$variableDetails$variableId, c('int7', 'cat5'))
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int11', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
df <- as.data.frame(testDF)
df$entity.int11 <- as.character(df$entity.int11)
makeCategoricalBin <- function(value) {veupathUtils::Bin('binLabel'=value)}
overlayBins <- veupathUtils::BinList(S4Vectors::SimpleList(lapply(as.character(c(1,2,3,4,5,6,7)), makeCategoricalBin)))
dt <- mapMarkers.dt(df, variables, value='count', xValues = overlayBins)
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(jsonList$mapMarkers$data$label[[1]], c("1","2","3","4","5","6","7","__UNSELECTED__"))
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(class(unlist(jsonList$mapMarkers$config$viewport)), 'NULL')
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cat5','int11'))
expect_equal(names(jsonList$sampleSizeTable), c('geoAggregateVariableDetails','xVariableDetails','size'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(class(jsonList$sampleSizeTable$xVariableDetails$value[[1]]), 'character')
expect_equal(jsonList$sampleSizeTable$xVariableDetails$variableId[1], 'int11')
expect_equal(names(jsonList$completeCasesTable), c('variableDetails','completeCases'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId'))
expect_equal(jsonList$completeCasesTable$variableDetails$variableId, c('int11', 'cat5'))
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'contA', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'NUMBER'),
dataShape = new("DataShape", value = 'CONTINUOUS'))
))
df <- as.data.frame(testDF)
overlayBins <- veupathUtils::getDiscretizedBins(df$entity.contA)
dt <- mapMarkers.dt(df, variables, value='count', xValues = overlayBins)
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(all(jsonList$mapMarkers$data$label[[5]] %in% unlist(lapply(overlayBins, function(x) {x@binLabel}))), TRUE)
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(class(unlist(jsonList$mapMarkers$config$viewport)), 'NULL')
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cat5','contA'))
# dont have sample sizes for x bc it was cont for the parent class :(
# map doesnt care so im not going to change it yet but stil...
expect_equal(names(jsonList$sampleSizeTable), c('geoAggregateVariableDetails','size'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(names(jsonList$completeCasesTable), c('variableDetails','completeCases'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId'))
expect_equal(jsonList$completeCasesTable$variableDetails$variableId, c('contA', 'cat5'))
# Ensure sampleSizeTable and completeCasesTable are not part of json if we do not ask for them.
dt <- mapMarkers.dt(df, variables, value='count', xValues = overlayBins, sampleSizes = FALSE, completeCases = FALSE)
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(names(jsonList$mapMarkers$config), c('variables','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(class(unlist(jsonList$mapMarkers$config$viewport)), 'NULL')
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cat5','contA'))
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
df <- as.data.frame(testDF)
dt <- mapMarkers.dt(df, variables, value='count')
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cat5','cat6'))
expect_equal(names(jsonList$sampleSizeTable), c('geoAggregateVariableDetails','xVariableDetails','size'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(class(jsonList$sampleSizeTable$xVariableDetails$value[[1]]), 'character')
expect_equal(jsonList$sampleSizeTable$xVariableDetails$variableId[1], 'cat6')
expect_equal(names(jsonList$completeCasesTable), c('variableDetails','completeCases'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId'))
expect_equal(jsonList$completeCasesTable$variableDetails$variableId, c('cat6', 'cat5'))
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
displayName = "panelLabel",
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
displayName = "xLabel",
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
dt <- mapMarkers.dt(df, variables, value='count')
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cat5','cat6'))
expect_equal(names(jsonList$sampleSizeTable), c('geoAggregateVariableDetails','xVariableDetails','size'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(jsonList$sampleSizeTable$geoAggregateVariableDetails$variableId[[1]], 'cat5')
expect_equal(class(jsonList$sampleSizeTable$xVariableDetails$value[[1]]), 'character')
expect_equal(jsonList$sampleSizeTable$xVariableDetails$variableId[[1]], 'cat6')
expect_equal(names(jsonList$completeCasesTable), c('variableDetails','completeCases'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId','displayLabel'))
expect_equal(jsonList$completeCasesTable$variableDetails$variableId, c('cat6', 'cat5'))
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
displayName = "panelLabel",
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
dt <- mapMarkers.dt(df, variables, value='count')
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers$data$geoAggregateVariableDetails), c('variableId','entityId','value','displayLabel'))
expect_equal(jsonList$mapMarkers$data$geoAggregateVariableDetails$variableId[[1]], 'cat5')
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cat5','cat6'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId','displayLabel'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(class(jsonList$sampleSizeTable$xVariableDetails$value[[1]]), 'character')
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int7', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'NUMBER'),
dataShape = new("DataShape", value = 'CONTINUOUS')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'NUMBER'),
dataShape = new("DataShape", value = 'CONTINUOUS'))
))
dt <- mapMarkers.dt(df, variables, value='count')
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('int7','int6'))
expect_equal(names(jsonList$sampleSizeTable), c('geoAggregateVariableDetails','xVariableDetails','size'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(class(jsonList$sampleSizeTable$xVariableDetails$value[[1]]), 'character')
expect_equal(names(jsonList$completeCasesTable), c('variableDetails','completeCases'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId'))
expect_equal(jsonList$completeCasesTable$variableDetails$variableId, c('int6', 'int7'))
# With continuous x var (< 9 values)
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'NUMBER'),
dataShape = new("DataShape", value = 'CONTINUOUS'))
))
df <- as.data.frame(testDF)
dt <- mapMarkers.dt(df, variables, value='count')
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cat5','int6'))
expect_equal(names(jsonList$sampleSizeTable), c('geoAggregateVariableDetails','xVariableDetails','size'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(class(jsonList$sampleSizeTable$xVariableDetails$value[[1]]), 'character')
expect_equal(jsonList$sampleSizeTable$xVariableDetails$variableId[1], 'int6')
expect_equal(names(jsonList$completeCasesTable), c('variableDetails','completeCases'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId'))
expect_equal(jsonList$completeCasesTable$variableDetails$variableId, c('int6', 'cat5'))
})
test_that("mapMarkers.dt() returns correct information about missing data", {
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat4', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int7', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
# Add nMissing missing values to each column
nMissing <- 10
df <- as.data.frame(lapply(testDF, function(x) {x[sample(1:length(x), nMissing, replace=F)] <- NA; x}))
dt <- mapMarkers.dt(df, variables, value='count')
completecasestable <- completeCasesTable(dt)
# Each entry should equal NROW(df) - nMissing
expect_equal(all(completecasestable$completeCases == nrow(df)-nMissing), TRUE)
# number of completeCases should be <= complete cases for each var
expect_equal(all(attr(dt, 'completeCasesAllVars')[1] <= completecasestable$completeCases), TRUE)
expect_equal(attr(dt, 'completeCasesAxesVars')[1] >= attr(dt, 'completeCasesAllVars')[1], TRUE)
dt <- mapMarkers.dt(df, variables, value='count', evilMode = 'strataVariables')
expect_equal(attr(dt, 'completeCasesAxesVars')[1], sum(!is.na(df$entity.contA)))
dt <- mapMarkers.dt(df, variables, value='count', evilMode = 'allVariables')
cols <- unlist(lapply(as.list(variables), function(x) {veupathUtils::getColName(x@variableSpec)}))
expect_equal(attr(dt, 'completeCasesAllVars')[1], sum(complete.cases(df[, cols, with=FALSE])))
# Numeric x
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat4', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'contA', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'NUMBER'),
dataShape = new("DataShape", value = 'CONTINUOUS'))
))
# Add nMissing missing values to each column
nMissing <- 10
df <- as.data.frame(lapply(testDF, function(x) {x[sample(1:length(x), nMissing, replace=F)] <- NA; x}))
overlayBins <- veupathUtils::getDiscretizedBins(df$entity.contA[complete.cases(df$entity.contA)])
dt <- mapMarkers.dt(df, variables, value='count', xValues = overlayBins)
completecasestable <- completeCasesTable(dt)
# Each entry should equal NROW(df) - nMissing
expect_equal(all(completecasestable$completeCases == nrow(df)-nMissing), TRUE)
# number of completeCases should be <= complete cases for each var
expect_equal(all(attr(dt, 'completeCasesAllVars')[1] <= completecasestable$completeCases), TRUE)
expect_equal(attr(dt, 'completeCasesAxesVars')[1] >= attr(dt, 'completeCasesAllVars')[1], TRUE)
dt <- mapMarkers.dt(df, variables, value='count', xValues = overlayBins, evilMode = 'strataVariables')
expect_equal(attr(dt, 'completeCasesAxesVars')[1], sum(!is.na(df$entity.contA)))
# TODO box cant have evilMode = 'allVariables' bc we cant calculate bins with NA
# dt <- mapMarkers.dt(df, variables, value='count', evilMode = 'allVariables')
# expect_equal(attr(dt, 'completeCasesAllVars')[1], sum(complete.cases(df[, map$id, with=FALSE])))
})
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context('mapMarkers')
test_that("mapMarkers.dt does not fail when there are no complete cases.", {
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'binary1', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
df <- data.noneComplete[is.na(entity.binary1),]
dt <- mapMarkers.dt(df, variables, value='count')
attr <- attributes(dt)
expect_equal(attr$completeCasesAllVars[1], 0)
expect_equal(is.list(dt$label), TRUE)
expect_equal(is.list(dt$value), TRUE)
dt <- mapMarkers.dt(df, variables, value='proportion')
attr <- attributes(dt)
expect_equal(attr$completeCasesAllVars[1], 0)
expect_equal(is.list(dt$label), TRUE)
expect_equal(is.list(dt$value), TRUE)
})
test_that("mapMarkers.dt() returns a valid plot.data mapMarkers object", {
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat4', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
df <- as.data.frame(testDF)
dt <- mapMarkers.dt(df, variables, value='count')
expect_is(dt, 'plot.data')
expect_is(dt, 'mapMarkers')
namedAttrList <- getPDAttributes(dt)
expect_equal(names(namedAttrList),c('variables', 'completeCasesAllVars','completeCasesAxesVars','completeCasesTable','sampleSizeTable','viewport'))
completeCases <- completeCasesTable(dt)
expect_equal(names(completeCases), c('variableDetails','completeCases'))
expect_equal(nrow(completeCases), 2)
sampleSizes <- sampleSizeTable(dt)
expect_equal(names(sampleSizes), c('entity.cat4','entity.cat6','size'))
expect_equal(nrow(sampleSizes), 4)
# Ensure sampleSizeTable and completeCasesTable do not get returned if we do not ask for them.
dt <- mapMarkers.dt(df, variables, value='count', sampleSizes = FALSE, completeCases = FALSE)
expect_is(dt, 'plot.data')
expect_is(dt, 'mapMarkers')
namedAttrList <- getPDAttributes(dt)
expect_equal(names(namedAttrList),c('variables','viewport'))
})
test_that("mapMarkers.dt() returns plot data and config of the appropriate types", {
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
df <- as.data.frame(testDF)
dt <- mapMarkers.dt(df, variables, value='count')
expect_is(dt$label, 'list')
expect_equal(class(unlist(dt$label)), 'character')
expect_is(dt$value, 'list')
expect_equal(class(unlist(dt$value)), 'integer')
namedAttrList <- getPDAttributes(dt)
expect_equal(class(namedAttrList$completeCasesAllVars),c('scalar', 'integer'))
expect_equal(class(namedAttrList$completeCasesAxesVars),c('scalar', 'integer'))
completeCases <- completeCasesTable(dt)
expect_equal(class(unlist(completeCases$variableDetails)), 'character')
expect_equal(class(unlist(completeCases$completeCases)), 'integer')
sampleSizes <- sampleSizeTable(dt)
expect_equal(class(unlist(sampleSizes$entity.cat5)), 'character')
expect_equal(class(unlist(sampleSizes$size)), 'integer')
})
test_that("mapMarkers.dt() returns an appropriately sized data.table", {
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat4', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
df <- as.data.frame(testDF)
dt <- mapMarkers.dt(df, variables, value='count')
expect_is(dt, 'data.table')
expect_is(dt, 'mapMarkers')
expect_equal(nrow(dt),4)
expect_equal(names(dt),c('entity.cat4', 'label', 'value'))
dt <- mapMarkers.dt(df, variables, value='proportion')
expect_is(dt, 'data.table')
expect_is(dt, 'mapMarkers')
expect_equal(nrow(dt),4)
expect_equal(names(dt),c('entity.cat4', 'label', 'value'))
expect_equal(all(grepl('.||.', dt$panel, fixed=T)), TRUE)
# sum of x counts within a group should sum to 1
expect_equal(all(lapply(dt$value, sum) == 1), TRUE)
# With factors
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'factor6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
dt <- mapMarkers.dt(df, variables, value='count')
expect_is(dt, 'data.table')
expect_is(dt, 'mapMarkers')
expect_equal(nrow(dt),6)
expect_equal(names(dt),c('entity.factor6', 'label', 'value'))
expect_equal(class(dt$entity.factor6), 'character')
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'factor6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
dt <- mapMarkers.dt(df, variables, value='count')
expect_is(dt, 'data.table')
expect_is(dt, 'mapMarkers')
expect_equal(nrow(dt),6)
expect_equal(names(dt),c('entity.factor6', 'label', 'value'))
expect_equal(class(dt$entity.factor6), 'character')
# With continuous x var (< 9 values)
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat4', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'NUMBER'),
dataShape = new("DataShape", value = 'CONTINUOUS'))
))
dt <- mapMarkers.dt(df, variables, value='count')
expect_is(dt, 'data.table')
expect_is(dt, 'mapMarkers')
expect_equal(nrow(dt),4)
expect_equal(names(dt),c('entity.cat4', 'label', 'value'))
dt <- mapMarkers.dt(df, variables, value='proportion')
expect_is(dt, 'data.table')
expect_is(dt, 'mapMarkers')
expect_equal(nrow(dt),4)
expect_equal(names(dt),c('entity.cat4', 'label', 'value'))
# sum of x counts within a group should sum to 1
expect_equal(all(lapply(dt$value, sum) == 1), TRUE)
})
test_that("mapMarkers() returns appropriately formatted json", {
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cont6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'longitude'),
dataType = new("DataType", value = 'LONGITUDE'),
dataShape = new("DataShape", value = 'CONTINUOUS')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cont5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'latitude'),
dataType = new("DataType", value = 'NUMBER'),
dataShape = new("DataShape", value = 'CONTINUOUS')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int7', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
df <- as.data.frame(testDF)
df$entity.int7 <- as.character(df$entity.int7)
viewport <- list('latitude'=list('xMin'=-.5,
'xMax'=.5),
'longitude'=list('left'=-.5,
'right'=.5))
dt <- mapMarkers.dt(df, variables, value='count', viewport=viewport)
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(class(unlist(jsonList$mapMarkers$config$viewport)), 'numeric')
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cont6','cont5','cat5','int7'))
expect_equal(names(jsonList$sampleSizeTable), c('geoAggregateVariableDetails','xVariableDetails','size'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(class(jsonList$sampleSizeTable$xVariableDetails$value[[1]]), 'character')
expect_equal(jsonList$sampleSizeTable$xVariableDetails$variableId[1], 'int7')
expect_equal(names(jsonList$completeCasesTable), c('variableDetails','completeCases'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId'))
expect_equal(jsonList$completeCasesTable$variableDetails$variableId, c('int7', 'cat5'))
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int11', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
df <- as.data.frame(testDF)
df$entity.int11 <- as.character(df$entity.int11)
makeCategoricalBin <- function(value) {veupathUtils::Bin('binLabel'=value)}
overlayBins <- veupathUtils::BinList(S4Vectors::SimpleList(lapply(as.character(c(1,2,3,4,5,6,7)), makeCategoricalBin)))
dt <- mapMarkers.dt(df, variables, value='count', xValues = overlayBins)
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(jsonList$mapMarkers$data$label[[1]], c("1","2","3","4","5","6","7","__UNSELECTED__"))
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(class(unlist(jsonList$mapMarkers$config$viewport)), 'NULL')
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cat5','int11'))
expect_equal(names(jsonList$sampleSizeTable), c('geoAggregateVariableDetails','xVariableDetails','size'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(class(jsonList$sampleSizeTable$xVariableDetails$value[[1]]), 'character')
expect_equal(jsonList$sampleSizeTable$xVariableDetails$variableId[1], 'int11')
expect_equal(names(jsonList$completeCasesTable), c('variableDetails','completeCases'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId'))
expect_equal(jsonList$completeCasesTable$variableDetails$variableId, c('int11', 'cat5'))
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'contA', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'NUMBER'),
dataShape = new("DataShape", value = 'CONTINUOUS'))
))
df <- as.data.frame(testDF)
overlayBins <- veupathUtils::getDiscretizedBins(df$entity.contA)
dt <- mapMarkers.dt(df, variables, value='count', xValues = overlayBins)
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(all(jsonList$mapMarkers$data$label[[5]] %in% unlist(lapply(overlayBins, function(x) {x@binLabel}))), TRUE)
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(class(unlist(jsonList$mapMarkers$config$viewport)), 'NULL')
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cat5','contA'))
# dont have sample sizes for x bc it was cont for the parent class :(
# map doesnt care so im not going to change it yet but stil...
expect_equal(names(jsonList$sampleSizeTable), c('geoAggregateVariableDetails','size'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(names(jsonList$completeCasesTable), c('variableDetails','completeCases'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId'))
expect_equal(jsonList$completeCasesTable$variableDetails$variableId, c('contA', 'cat5'))
# Ensure sampleSizeTable and completeCasesTable are not part of json if we do not ask for them.
dt <- mapMarkers.dt(df, variables, value='count', xValues = overlayBins, sampleSizes = FALSE, completeCases = FALSE)
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(names(jsonList$mapMarkers$config), c('variables','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(class(unlist(jsonList$mapMarkers$config$viewport)), 'NULL')
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cat5','contA'))
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
df <- as.data.frame(testDF)
dt <- mapMarkers.dt(df, variables, value='count')
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cat5','cat6'))
expect_equal(names(jsonList$sampleSizeTable), c('geoAggregateVariableDetails','xVariableDetails','size'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(class(jsonList$sampleSizeTable$xVariableDetails$value[[1]]), 'character')
expect_equal(jsonList$sampleSizeTable$xVariableDetails$variableId[1], 'cat6')
expect_equal(names(jsonList$completeCasesTable), c('variableDetails','completeCases'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId'))
expect_equal(jsonList$completeCasesTable$variableDetails$variableId, c('cat6', 'cat5'))
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
displayName = "panelLabel",
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
displayName = "xLabel",
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
dt <- mapMarkers.dt(df, variables, value='count')
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cat5','cat6'))
expect_equal(names(jsonList$sampleSizeTable), c('geoAggregateVariableDetails','xVariableDetails','size'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(jsonList$sampleSizeTable$geoAggregateVariableDetails$variableId[[1]], 'cat5')
expect_equal(class(jsonList$sampleSizeTable$xVariableDetails$value[[1]]), 'character')
expect_equal(jsonList$sampleSizeTable$xVariableDetails$variableId[[1]], 'cat6')
expect_equal(names(jsonList$completeCasesTable), c('variableDetails','completeCases'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId','displayLabel'))
expect_equal(jsonList$completeCasesTable$variableDetails$variableId, c('cat6', 'cat5'))
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
displayName = "panelLabel",
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
dt <- mapMarkers.dt(df, variables, value='count')
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers$data$geoAggregateVariableDetails), c('variableId','entityId','value','displayLabel'))
expect_equal(jsonList$mapMarkers$data$geoAggregateVariableDetails$variableId[[1]], 'cat5')
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cat5','cat6'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId','displayLabel'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(class(jsonList$sampleSizeTable$xVariableDetails$value[[1]]), 'character')
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int7', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'NUMBER'),
dataShape = new("DataShape", value = 'CONTINUOUS')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'NUMBER'),
dataShape = new("DataShape", value = 'CONTINUOUS'))
))
dt <- mapMarkers.dt(df, variables, value='count')
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('int7','int6'))
expect_equal(names(jsonList$sampleSizeTable), c('geoAggregateVariableDetails','xVariableDetails','size'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(class(jsonList$sampleSizeTable$xVariableDetails$value[[1]]), 'character')
expect_equal(names(jsonList$completeCasesTable), c('variableDetails','completeCases'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId'))
expect_equal(jsonList$completeCasesTable$variableDetails$variableId, c('int6', 'int7'))
# With continuous x var (< 9 values)
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat5', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int6', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'NUMBER'),
dataShape = new("DataShape", value = 'CONTINUOUS'))
))
df <- as.data.frame(testDF)
dt <- mapMarkers.dt(df, variables, value='count')
outJson <- getJSON(dt, FALSE)
jsonList <- jsonlite::fromJSON(outJson)
expect_equal(names(jsonList), c('mapMarkers','sampleSizeTable','completeCasesTable'))
expect_equal(names(jsonList$mapMarkers), c('data','config'))
expect_equal(names(jsonList$mapMarkers$data), c('geoAggregateVariableDetails','label','value'))
expect_equal(names(jsonList$mapMarkers$config), c('variables','completeCasesAllVars','completeCasesAxesVars','viewport'))
expect_equal(names(jsonList$mapMarkers$config$variables$variableSpec), c('variableId','entityId'))
expect_equal(jsonList$mapMarkers$config$variables$variableSpec$variableId, c('cat5','int6'))
expect_equal(names(jsonList$sampleSizeTable), c('geoAggregateVariableDetails','xVariableDetails','size'))
expect_equal(class(jsonList$sampleSizeTable$geoAggregateVariableDetails$value[[1]]), 'character')
expect_equal(class(jsonList$sampleSizeTable$xVariableDetails$value[[1]]), 'character')
expect_equal(jsonList$sampleSizeTable$xVariableDetails$variableId[1], 'int6')
expect_equal(names(jsonList$completeCasesTable), c('variableDetails','completeCases'))
expect_equal(names(jsonList$completeCasesTable$variableDetails), c('variableId','entityId'))
expect_equal(jsonList$completeCasesTable$variableDetails$variableId, c('int6', 'cat5'))
})
test_that("mapMarkers.dt() returns correct information about missing data", {
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat4', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'int7', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL'))
))
# Add nMissing missing values to each column
nMissing <- 10
df <- as.data.frame(lapply(testDF, function(x) {x[sample(1:length(x), nMissing, replace=F)] <- NA; x}))
dt <- mapMarkers.dt(df, variables, value='count')
completecasestable <- completeCasesTable(dt)
# Each entry should equal NROW(df) - nMissing
expect_equal(all(completecasestable$completeCases == nrow(df)-nMissing), TRUE)
# number of completeCases should be <= complete cases for each var
expect_equal(all(attr(dt, 'completeCasesAllVars')[1] <= completecasestable$completeCases), TRUE)
expect_equal(attr(dt, 'completeCasesAxesVars')[1] >= attr(dt, 'completeCasesAllVars')[1], TRUE)
dt <- mapMarkers.dt(df, variables, value='count', evilMode = 'strataVariables')
expect_equal(attr(dt, 'completeCasesAxesVars')[1], sum(!is.na(df$entity.contA)))
dt <- mapMarkers.dt(df, variables, value='count', evilMode = 'allVariables')
cols <- unlist(lapply(as.list(variables), function(x) {veupathUtils::getColName(x@variableSpec)}))
expect_equal(attr(dt, 'completeCasesAllVars')[1], sum(complete.cases(df[, cols, with=FALSE])))
# Numeric x
variables <- new("VariableMetadataList", SimpleList(
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'cat4', entityId = 'entity'),
plotReference = new("PlotReference", value = 'geo'),
dataType = new("DataType", value = 'STRING'),
dataShape = new("DataShape", value = 'CATEGORICAL')),
new("VariableMetadata",
variableClass = new("VariableClass", value = 'native'),
variableSpec = new("VariableSpec", variableId = 'contA', entityId = 'entity'),
plotReference = new("PlotReference", value = 'xAxis'),
dataType = new("DataType", value = 'NUMBER'),
dataShape = new("DataShape", value = 'CONTINUOUS'))
))
# Add nMissing missing values to each column
nMissing <- 10
df <- as.data.frame(lapply(testDF, function(x) {x[sample(1:length(x), nMissing, replace=F)] <- NA; x}))
overlayBins <- veupathUtils::getDiscretizedBins(df$entity.contA[complete.cases(df$entity.contA)])
dt <- mapMarkers.dt(df, variables, value='count', xValues = overlayBins)
completecasestable <- completeCasesTable(dt)
# Each entry should equal NROW(df) - nMissing
expect_equal(all(completecasestable$completeCases == nrow(df)-nMissing), TRUE)
# number of completeCases should be <= complete cases for each var
expect_equal(all(attr(dt, 'completeCasesAllVars')[1] <= completecasestable$completeCases), TRUE)
expect_equal(attr(dt, 'completeCasesAxesVars')[1] >= attr(dt, 'completeCasesAllVars')[1], TRUE)
dt <- mapMarkers.dt(df, variables, value='count', xValues = overlayBins, evilMode = 'strataVariables')
expect_equal(attr(dt, 'completeCasesAxesVars')[1], sum(!is.na(df$entity.contA)))
# TODO box cant have evilMode = 'allVariables' bc we cant calculate bins with NA
# dt <- mapMarkers.dt(df, variables, value='count', evilMode = 'allVariables')
# expect_equal(attr(dt, 'completeCasesAllVars')[1], sum(complete.cases(df[, map$id, with=FALSE])))
})
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