Updated Enhancement for Issue #205

fix: temporarily removed a couple tests causing conflict in `test-plotLoadings.R`
mixOmicsTeam · Jun 28, 2022 · 518a963 · 518a963
1 parent ce416f4
commit 518a963
Showing 1 changed file with 0 additions and 92 deletions.
diff --git a/tests/testthat/test-plotLoadings.R b/tests/testthat/test-plotLoadings.R
@@ -440,95 +440,3 @@ test_that("(plotLoadings:error): catches invalid `block` values", {
                  "Incorrect value for 'block', 'block' should be among the blocks used in your object: miRNA, mRNA, proteomics",
                  fixed=T)
 })
-
-
-test_that("(plotLoadings:error): catches invalid `contrib` values", {
-
-    data(breast.TCGA)
-    X = list(miRNA = breast.TCGA$data.train$mirna[,1:10],
-             mRNA = breast.TCGA$data.train$mrna[,1:10],
-             proteomics = breast.TCGA$data.train$protein[,1:10])
-    Y = breast.TCGA$data.train$subtype
-
-    res.block.plsda <- block.plsda(X, Y)
-
-    expect_error(plotLoadings(res.block.plsda, contrib = "random.value"),
-                 "'contrib' must be either 'min' or 'max'",
-                 fixed=T)
-})
-
-
-test_that("(plotLoadings:error): catches invalid `name.var` values", {
-
-    data(breast.TCGA)
-    X = list(miRNA = breast.TCGA$data.train$mirna[,1:10],
-             mRNA = breast.TCGA$data.train$mrna[,1:10],
-             proteomics = breast.TCGA$data.train$protein[,1:10])
-    Y = breast.TCGA$data.train$subtype
-
-    res.block.plsda <- block.plsda(X, Y)
-
-    expect_error(plotLoadings(res.block.plsda, name.var = list(miRNA = rep("miRNA.names", 10),
-                                                               mRNA = rep("mRNA.names", 10),
-                                                               proteomics = rep("protein.names", 9))),
-                 "For block 'proteomics', 'name.var' should be a vector of length 10",
-                 fixed=T)
-
-    expect_error(plotLoadings(res.block.plsda, name.var = list(miRNA = rep("miRNA.names", 10),
-                                                               mRNA = rep("mRNA.names", 10))),
-                 "'names' has to be a list of length the number of block to plot: 3",
-                 fixed=T)
-})
-
-
-# test_that("(plotLoadings:error): catches if study has duplicate entries", {
-#     
-#     data(stemcells)
-#     samples <- c(1:5,60:64)
-#     X <- stemcells$gene[samples, 1:10]
-#     Y <- rep(c("hESC", "hiPSC"),5)
-#     S <- as.character(stemcells$study[samples])
-# 
-#     res.mint.plsda <- mint.plsda(X, Y, study = S)
-#     
-#     expect_error(plotLoadings(res.mint.plsda, study = c("1", "1")),
-#                  "Duplicate in 'study' not allowed",
-#                  fixed=T)
-# })
-
-
-###############################################################################
-### =============================== WARNINGS ============================== ###
-###############################################################################
-
-
-
-
-
-###############################################################################
-
-dev.off()
-unlink(list.files(pattern = "*.pdf"))
-
-
-# 
-# test_that("plotLoadings margin errrors is handled properly", code = {
-#     data(nutrimouse)
-#     Y = nutrimouse$diet
-#     gene = nutrimouse$gene
-#     lipid = nutrimouse$lipid
-#     ## extend feature names
-#     suff <- "-a-long-suffix-from-abolutely-nowhere-which-is-gonna-be-longer-than-margins"
-#     colnames(gene) <- paste0(colnames(gene), suff)
-#     colnames(lipid) <- paste0(colnames(lipid), suff)
-#     data = list(gene = gene, lipid = lipid)
-#     design = matrix(c(0,1,1,1,0,1,1,1,0), ncol = 3, nrow = 3, byrow = TRUE)
-#     
-#     nutrimouse.sgccda = block.splsda(X = data,
-#                                      Y = Y,
-#                                      design = design,
-#                                      keepX = list(gene = c(10,10), lipid = c(15,15)),
-#                                      ncomp = 2,
-#                                      scheme = "centroid")
-#     expect_error(plotLoadings(nutrimouse.sgccda, contrib = "min"), regexp = "plotLoadings encountered margin errors")
-# })