Nothing
test_that("clusterProfiler input is accepted", {
enrich <- clusterProfilerGSEA()
expect_no_error(data <- prepareEnrichment(enrich@result, requireTheme = FALSE))
expect_no_error(data <- prepareEnrichment(enrich@result, requireTheme = TRUE))
enrich <- clusterProfilerORA()
expect_no_error(data <- prepareEnrichment(enrich@result, requireTheme = FALSE))
# Adjust theme for ORA
theme <- aPEAR.theme
theme$colorBy <- 'pvalue'
theme$nodeSize <- 'Count'
expect_no_warning(data <- prepareEnrichment(enrich@result, requireTheme = TRUE, theme = theme))
})
test_that("custom input is accepted", {
enrich <- customEnrichment()
expect_no_error(data <- prepareEnrichment(enrich, requireTheme = FALSE))
expect_error(data <- prepareEnrichment(enrich, requireTheme = TRUE))
theme <- aPEAR.theme
theme$colorBy <- 'nes'
theme$nodeSize <- 'size'
expect_no_error(data <- prepareEnrichment(enrich, requireTheme = TRUE, theme = theme))
})
test_that("pathways are ranked correctly when clusterName 'nes' or 'pval'", {
# Least important pathway should have lowest score (min NES and max pval)
enrich <- clusterProfilerGSEA()
methods <- aPEAR.methods
methods$clusterName <- 'nes'
methods$clusterNameColumn <- 'NES'
data <- prepareEnrichment(enrich@result, requireTheme = FALSE, methods = methods)
expect_true(all(data$enrichment[ , Ranks ] %in% 1:nrow(enrich@result)))
expect_true(data$enrichment[ which.min(abs(NES)), Ranks ] == 1)
expect_true(data$enrichment[ which.max(abs(NES)), Ranks ] == nrow(enrich@result))
methods <- aPEAR.methods
methods$clusterName <- 'pval'
methods$clusterNameColumn <- 'pvalue'
data <- prepareEnrichment(enrich@result, requireTheme = FALSE, methods = methods)
expect_true(all(data$enrichment[ , Ranks ] %in% 1:nrow(enrich@result)))
expect_true(1 %in% data$enrichment[ pvalue == max(pvalue), Ranks ])
expect_true(nrow(enrich@result) %in% data$enrichment[ pvalue == min(pvalue), Ranks ])
})
test_that("theme parameters are adjusted for clusterProfiler ORA", {
enrich <- clusterProfilerORA()
suppressWarnings(expect_no_error(data <- prepareEnrichment(enrich@result, requireTheme = TRUE)))
theme <- aPEAR.theme
theme$colorBy <- 'pvalue'
theme$colorType <- 'pval'
expect_warning(data <- prepareEnrichment(enrich@result, requireTheme = TRUE, theme = theme))
expect_true(data$enrichment[ , min(Color) ] <= theme$pCutoff)
expectColors <- log10(enrich@result[ , c('pvalue') ])
expectColors[ expectColors <= theme$pCutoff ] <- theme$pCutoff
expect_true(all(data$enrichment[ , list(Color) ] == expectColors))
expect_true(all(data$enrichment[ , list(Size) ] == enrich@result[ , c('Count') ]))
theme <- aPEAR.theme
theme$nodeSize <- 'Count'
expect_warning(data <- prepareEnrichment(enrich@result, requireTheme = TRUE, theme = theme))
expect_true(data$enrichment[ , min(Color) ] <= theme$pCutoff)
expectColors <- log10(enrich@result[ , c('pvalue') ])
expectColors[ expectColors <= theme$pCutoff ] <- theme$pCutoff
expect_true(all(data$enrichment[ , Color ] == expectColors))
expect_true(all(data$enrichment[ , Size ] == enrich@result[ , c('Count') ]))
})
test_that("theme parameters are adjusted for clusterProfiler GSEA", {
enrich <- clusterProfilerGSEA()
expect_no_error(data <- prepareEnrichment(enrich@result, requireTheme = TRUE))
expect_true(all(data$enrichment[ , Color ] == enrich@result[ , 'NES' ]))
expect_true(all(data$enrichment[ , Size ] == enrich@result[ , 'setSize' ]))
})
test_that("theme parameters are adjusted for gProfiler", {
enrich <- gprofilerEnrichment()
enrich <- enrich$result
suppressWarnings(expect_warning(expect_no_error(data <- prepareEnrichment(enrich))))
# Make sure the original data remains unchanged
expect_true(!('Description' %in% colnames(enrich)))
theme <- aPEAR.theme
expectColors <- log10(enrich[ , c('p_value') ])
expectColors[ expectColors <= theme$pCutoff ] <- theme$pCutoff
expect_true(all(data$enrichment[ , list(Color) ] == expectColors))
expect_true(all(data$enrichment[ , list(Size) ] == enrich[ , c('term_size') ]))
theme <- aPEAR.theme
theme$nodeSize <- 'query_size'
expect_warning(data <- prepareEnrichment(enrich, requireTheme = TRUE, theme = theme))
expect_true(data$enrichment[ , min(Color) ] <= theme$pCutoff)
expect_true(all(data$enrichment[ , list(Size) ] == enrich[ , c('query_size') ]))
theme <- aPEAR.theme
theme$colorBy <- 'intersection_size'
expect_warning(data <- prepareEnrichment(enrich, requireTheme = TRUE, theme = theme))
expect_true(all(data$enrichment[ , list(Color) ] == enrich[ , c('intersection_size') ]))
})
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