tests/testthat/test-PlotGeneSet.R

In HajkD/myTAI: Evolutionary Transcriptomics

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
        ))
})