Nothing
context("Test: PlotGeneSet() ")
# http://stats.stackexchange.com/questions/118033/best-series-of-colors-to-use-for-differentiating-series-in-publication-quality
equal_df <- function(df1, df2) {
rownames(df1) <- NULL
rownames(df2) <- NULL
isTRUE(all.equal(df1, df2))
}
data(PhyloExpressionSetExample)
nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]
example.geneset <-
PhyloExpressionSetExample[sample(1:22000, 10) , 2]
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"
)
TestSubSet <-
PhyloExpressionSetExample[match(tolower(genes_example), tolower(PhyloExpressionSetExample[, 2])),]
test_that("is.ExpressionSet() throughs error when no ExpressionSet is entered to PlotGeneSet()",
{
expect_error(
PlotGeneSet(nonStandardExpressionSet, example.geneset)
)
})
test_that("Number of colors and number of input genes are equal when colors are specified..",
{
expect_error(
PlotGeneSet(
PhyloExpressionSetExample,
genes_example,
colors = rainbow(10),
get.subset = TRUE
),
"The number of colors and the number of genes do not match."
)
})
test_that("Missing genes are reported by warning....", {
expect_warning(
PlotGeneSet(
PhyloExpressionSetExample,
missing_genes_example,
get.subset = TRUE
),
"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(
PlotGeneSet(
PhyloExpressionSetExample,
all_missing_genes_example
) ,
"None of your input gene ids could be found in the ExpressionSet."
)
})
test_that("PlotGeneSet() returns the correct subset of genes..", {
expect_true(equal_df(
PlotGeneSet(
PhyloExpressionSetExample,
genes_example,
get.subset = TRUE
),
TestSubSet
))
})
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