PR addressing Issue #150 (#184)

enhance: adds checks to `plotArrow()` to prevent single-omics and P-integrative methods to be visualised

The file allows for testing of the `plotArrow()` function. Two included tests check for general functionality on DIABLO objects as well as inability to function on `(mint).(s)plsda` objects

R/plotArrow.R

@@ -70,7 +70,11 @@ plotArrow <- function(object,
     object.blocks=c("sgcca", "sgccda", "rgcca")
 
     if (! any(class.object %in% c(object.pls,object.blocks)))
-        stop( " 'plotArrow' is only implemented for the following objects: pls, plsda, spls, splsda, rcc, sgcca, sgccda, rgcca", call.=FALSE)
+        stop( " 'plotArrow' is only implemented for the following objects: pls, spls, rcc, sgcca, sgccda, rgcca", call.=FALSE)
+
+    if ("DA" %in% class.object && !any(object.blocks %in% class.object)) {
+        stop("'plotArrow' not implemented for (s)PLSDA or MINT sPLSDA", call.=FALSE)
+    }
 
     ind.names.position <- match.arg(ind.names.position)
     is.multiblock <- ifelse(is.list(object$X), TRUE, FALSE)

tests/testthat/test-plotArrow.R

@@ -0,0 +1,38 @@
+test_that("plotArrow does not function on (mint).(s).plsda objects", code = {
+
+  data("stemcells")
+
+  X <- stemcells$gene
+  Y <- stemcells$celltype
+  S <- stemcells$study
+
+  optimal.ncomp <- 4
+  optimal.keepX <- c(24, 45, 20, 30)
+
+  splsda.stemcells <- splsda(X = X, Y = Y, 
+                             ncomp = optimal.ncomp, 
+                             keepX = optimal.keepX)
+  expect_error(plotArrow(splsda.stemcells), "'plotArrow' not implemented for (s)PLSDA or MINT sPLSDA", fixed = TRUE)
+})
+
+test_that("plotArrow functions on DIABLO objects", code = {
+
+  data(breast.TCGA)
+
+  X <- list(miRNA = breast.TCGA$data.train$mirna, 
+            mRNA = breast.TCGA$data.train$mrna,
+            proteomics = breast.TCGA$data.train$protein)
+  Y <- breast.TCGA$data.train$subtype
+
+  optimal.ncomp <- 2
+  optimal.keepX <-  list(miRNA = c(10, 5), 
+                         mRNA = c(25,16),
+                         proteomics = c(8,5))
+  tcga.diablo <- block.splsda(X, Y,
+                              ncomp = optimal.ncomp,
+                              keepX = optimal.keepX)
+
+  pA_res <- plotArrow(tcga.diablo)
+
+  expect_is(pA_res, "ggplot")
+})