Nothing
context("Test: PlotEnrichment() ")
# http://stats.stackexchange.com/questions/72553/which-statistical-test-should-be-used-to-test-for-enrichment-of-gene-lists
# http://en.wikipedia.org/wiki/Fisher%27s_exact_test
equal_df <- function(df1, df2) {
rownames(df1) <- NULL
rownames(df2) <- NULL
isTRUE(all.equal(df1, df2))
}
missing_genes_example <-
c(
"AT4G22950.1",
"AT4G24540.1",
"AT1G69120.1",
"AT5G15840.1",
"AT4G35900.1",
"AT5G10140.1",
"AT4G00650.1",
"AT1G65480.1",
"AT1G22770.1",
"AT5G61850.1",
"AT2G45660",
"AT5G03840"
)
all_missing_genes_example <-
c("AT1G22770", "AT5G61850", "AT2G45660", "AT5G03840")
genes_example <-
c(
"AT4G22950.1",
"AT4G24540.1",
"AT1G69120.1",
"AT5G15840.1",
"AT4G35900.1",
"AT5G10140.1",
"AT4G00650.1",
"AT1G65480.1",
"AT1G22770.1",
"AT5G61850.1",
"AT2G45660.1",
"AT5G03840.1"
)
data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)
set.seed(123)
test_set <- sample(PhyloExpressionSetExample[, 2], 22000)
nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]
test_that(
"is.ExpressionSet() throughs error when no ExpressionSet is entered to PlotEnrichment()",
{
expect_error(
PlotEnrichment(nonStandardExpressionSet, test_set, legendName = "PS")
)
}
)
test_that(
"error occurs when test.set inlcudes more genes than are available in the
input ExpressionSet",
{
expect_error(
PlotEnrichment(PhyloExpressionSetExample[sample(1:22000, 19000), ], test_set, legendName = "PS") ,
"Your input GeneID vector stores more elements than are available in your ExpressionSet object..."
)
}
)
test_that("Missing genes are reported by warning....", {
expect_warning(
PlotEnrichment(
PhyloExpressionSetExample,
missing_genes_example,
legendName = "PS",
plot.bars = FALSE
),
"Only 10 out of your 12 gene ids could be found in the ExpressionSet."
)
})
test_that("Error occurs when none of the input gene ids match with the ExpressionSet object",
{
expect_error(
PlotEnrichment(
PhyloExpressionSetExample,
all_missing_genes_example,
legendName = "PS"
) ,
"None of your input gene ids could be found in the ExpressionSet."
)
})
TestSetPS1_3 <-
PhyloExpressionSetExample[which(PhyloExpressionSetExample[, 1] %in% c(1, 2, 3)), 2]
TestSetPS1_2 <-
PhyloExpressionSetExample[which(PhyloExpressionSetExample[, 1] %in% c(1, 2)), 2]
TestSetPS1 <-
PhyloExpressionSetExample[which(PhyloExpressionSetExample[, 1] %in% c(1)), 2]
test_that("PlotEnrichment() executes with only 3 out of 12 PS present in the test.set",
{
expect_true(all(which(
PlotEnrichment(
PhyloExpressionSetExample,
TestSetPS1_3,
measure = "log-foldchange",
legendName = "PS",
plot.bars = FALSE
)$enrichment.matrix[4:12 , 2] == 0
)))
expect_true(all(which(
PlotEnrichment(
PhyloExpressionSetExample,
TestSetPS1_3,
measure = "log-foldchange",
legendName = "PS",
plot.bars = FALSE
)$enrichment.matrix[1:3 , 2] > 0
)))
expect_true(all(which(
PlotEnrichment(
PhyloExpressionSetExample,
TestSetPS1_3,
measure = "foldchange",
legendName = "PS",
plot.bars = FALSE
)$enrichment.matrix[4:12 , 2] == 0
)))
expect_true(all(which(
PlotEnrichment(
PhyloExpressionSetExample,
TestSetPS1_3,
measure = "foldchange",
legendName = "PS",
plot.bars = FALSE
)$enrichment.matrix[1:3 , 2] > 0
)))
})
test_that("PlotEnrichment() executes with only 2 out of 12 PS present in the test.set",
{
expect_true(all(which(
PlotEnrichment(
PhyloExpressionSetExample,
TestSetPS1_2,
measure = "log-foldchange",
legendName = "PS",
plot.bars = FALSE
)$enrichment.matrix[4:12 , 2] == 0
)))
expect_true(all(which(
PlotEnrichment(
PhyloExpressionSetExample,
TestSetPS1_2,
measure = "log-foldchange",
legendName = "PS",
plot.bars = FALSE
)$enrichment.matrix[1:3 , 2] > 0
)))
expect_true(all(which(
PlotEnrichment(
PhyloExpressionSetExample,
TestSetPS1_2,
measure = "foldchange",
legendName = "PS",
plot.bars = FALSE
)$enrichment.matrix[4:12 , 2] == 0
)))
expect_true(all(which(
PlotEnrichment(
PhyloExpressionSetExample,
TestSetPS1_2,
measure = "foldchange",
legendName = "PS",
plot.bars = FALSE
)$enrichment.matrix[1:3 , 2] > 0
)))
})
test_that("PlotEnrichment() executes with only 1 out of 12 PS present in the test.set",
{
expect_true(all(which(
PlotEnrichment(
PhyloExpressionSetExample,
TestSetPS1,
measure = "log-foldchange",
legendName = "PS",
plot.bars = FALSE
)$enrichment.matrix[4:12 , 2] == 0
)))
expect_true(all(which(
PlotEnrichment(
PhyloExpressionSetExample,
TestSetPS1,
measure = "log-foldchange",
legendName = "PS",
plot.bars = FALSE
)$enrichment.matrix[1:3 , 2] > 0
)))
expect_true(all(which(
PlotEnrichment(
PhyloExpressionSetExample,
TestSetPS1,
measure = "foldchange",
legendName = "PS",
plot.bars = FALSE
)$enrichment.matrix[4:12 , 2] == 0
)))
expect_true(all(which(
PlotEnrichment(
PhyloExpressionSetExample,
TestSetPS1,
measure = "foldchange",
legendName = "PS",
plot.bars = FALSE
)$enrichment.matrix[1:3 , 2] > 0
)))
})
# construct an example PhyloExpressionSet
PES.Test <- data.frame(
PS = c(
rep(1, 4),
rep(2, 2),
rep(3, 6),
rep(4, 1),
rep(5, 12),
rep(6, 3),
rep(7, 3)
),
GeneID = paste0("AT", 1:31),
stringsAsFactors = FALSE
)
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