test_11plotting.R
In MEAL: Perform methylation analysis

# context("Plotting")
# 
# library(minfiData)
# set <- prepareMethylationSet(getBeta(MsetEx)[1:10,], pheno = data.frame(pData(MsetEx)))
# methyOneVar <- DAPipeline(set, variable_names = "sex", probe_method = "ls")
# methyTwoVar <- DAPipeline(set, variable_names =  "person", probe_method = "ls")
# 
# range <- GenomicRanges::GRanges(seqnames=Rle("chrY"), 
#                                 ranges = IRanges(3000000, end=12300000))
# rangeNoSNPs <- DARegionAnalysis(set, variable_names = "sex", range = range)
# 
# eset <- ExpressionSet(matrix(runif(12, max = 15), 3))
# annot <- data.frame(chromosome = rep("chrY", 3), start = c(10000, 4500000, 5000000), 
#                     end = c(100090, 6000000, 90000000))
# fData(eset) <- annot
# pData(eset) <- data.frame(sex = c("H", "M", "H", "M"))
# esetRes <- DAPipeline(eset, variable_names = "sex", probe_method = "ls")
# 
# test_that("Plot CPGs",{
#   expect_error(plotFeature(methyOneVar, 12351413654), "feat index must be greater than 0 and smaller than the number of features.")
#   expect_error(plotFeature(methyOneVar, -12), "feat index must be greater than 0 and smaller than the number of features.")
#   expect_error(plotFeature(methyOneVar, 1, variables = character()), "variables must have one or two values.")
#   expect_error(plotFeature(methyOneVar, 1, variables = "character"),"Not all variables are present in set phenodata.")
#   expect_error(plotFeature(methyOneVar, 1, variables = c("age", "sex", "status")), "variables must have one or two values.")
#   expect_error(plotFeature(methyOneVar, "12"), "feat name is not present in the set.")
#   expect_error(plotFeature(methyOneVar, numeric()), "feat must contain only one value.")
#   expect_error(plotFeature(methyOneVar, 1:5), "feat must contain only one value.")
#   expect_error(plotFeature(MsetEx, 12, "age"), "set must be of class AnalysisResults, MethylationSet or ExpressionSet")
#   expect_error(plotBestFeatures(MsetEx, 12, "age"), "set must be of class AnalysisResults, ExpressionSet or MethylationSet")
#   expect_warning(plotBestFeatures(rangeNoSNPs, 12421531461, "sex"), "n is greater than the number of betas present in the set.")
# })
# 
# test_that("Plot Ewas", {
#   expect_error(plotEWAS(methyOneVar, variable = character()), "variable must have one value.")
#   expect_error(plotEWAS(methyOneVar, variable = c("a", "b")), "variable must have one value.")
#   expect_error(plotEWAS(methyOneVar, variable = "a"), "Variable is not present in the model.")
#   expect_warning(plotEWAS(rangeNoSNPs), "For a better visualization of the region, use plotRegion.")
#   plotEWAS(methyOneVar)
# })
# 
# test_that("Plot Volcano", {
#   plotVolcano(methyOneVar)
#   expect_error(plotVolcano(methyOneVar, variable = character()), "variable must have one value.")
#   expect_error(plotVolcano(methyOneVar, variable = c("a", "b")), "variable must have one value.")
#   expect_error(plotVolcano(methyOneVar, variable = "a"), "Variable is not present in the model.")
# })
# 
# test_that("QQPlot", {
#   expect_error(plotQQ(methyOneVar, variable = character()), "variable must have one value.")
#   expect_error(plotQQ(methyOneVar, variable = c("a", "b")), "variable must have one value.")
#   expect_error(plotQQ(methyOneVar, variable = "a"), "Variable is not present in phenodata.")
#   expect_warning(plotQQ(rangeNoSNPs), "QQplot is not recommended in range analyis.")
# })
# 
# test_that("plotRDA", {
#   expect_error(plotRDA(rangeNoSNPs, n_feat = -1), "n_feat must be greater than 1.")
#   expect_warning(plotRDA(rangeNoSNPs, n_feat = 9999), "n_feat is greater than the total number of features in the range.")
# })
# 
# test_that("Plot Region", {
#   expect_error(plotRegion(rangeNoSNPs, variable = character()), "variable must have one value.")
#   expect_error(plotRegion(rangeNoSNPs, variable = c("a", "b")), "variable must have one value.")
#   expect_error(plotRegion(rangeNoSNPs, variable = "a"), "Variable is not present in modelVariables.\nValid variables are sex")
#   expect_error(plotRegion(methyOneVar), "range must be present to use plotRegion with a AnalysisResults")
#   expect_error(plotRegion(esetRes), "Results must have a column called position to perform this plot.")
#   plotRegion(rangeNoSNPs)
# })
# 
# dev.off()
# file.remove("Rplots.pdf")