Updated fix for Issue #120

test: added test case for `mint.(s)pls` in `test-plotLoadings.R` to ensure coverage of diff

also adjusted `is()` calls to `inherits()` to see if this solves `vignette.Rmd` issue - unlikely

R/plotLoadings.R

@@ -967,10 +967,10 @@ check.input.plotLoadings <- function(object,
     # --
     if (missing(block))
     {
-        if (!is(object, "DA"))
+        if (!inherits(object, "DA"))
         {
             block = object$names$blocks
-        } else  if (is(object, c("mixo_plsda", "mixo_splsda"))) {
+        } else  if (inherits(object, c("mixo_plsda", "mixo_splsda"))) {
             block = "X"
         } else {
             if (!is.null(object$indY))
@@ -982,17 +982,17 @@ check.input.plotLoadings <- function(object,
         }
     }
 
-    if (is(object, c("mixo_plsda", "mixo_splsda")) & (!all(block %in% c(1,"X")) | length(block) > 1 ))
+    if (inherits(object, c("mixo_plsda", "mixo_splsda")) & (!all(block %in% c(1,"X")) | length(block) > 1 ))
         stop("'block' can only be 'X' or '1' for plsda and splsda object")
 
-    if (is(object, c("mixo_plsda", "mixo_splsda","pca")))
+    if (inherits(object, c("mixo_plsda", "mixo_splsda","pca")))
     {
         object$indY = 2
-    } else if (is(object, c("mixo_pls", "mixo_spls"))) {
+    } else if (inherits(object, c("mixo_pls", "mixo_spls"))) {
         object$indY = 3 # we don't want to remove anything in that case, and 3 is higher than the number of blocks which is 2
     }
 
-    if(!is(object, "DA"))
+    if(!inherits(object, "DA"))
         object$indY = length(object$names$blocks)+1  # we don't want to remove anything in that case, and 3 is higher than the number of blocks which is 2
 
     if(is.numeric(block))
@@ -1203,7 +1203,7 @@ get.loadings.ndisplay <- function(object,
 
     #comp
     # ----
-    if (is(object, c("mixo_pls","mixo_spls", "rcc")))# cause pls methods just have 1 ncomp, block approaches have different ncomp per block
+    if (inherits(object, c("mixo_pls","mixo_spls", "rcc")))# cause pls methods just have 1 ncomp, block approaches have different ncomp per block
     {
         ncomp = object$ncomp
         object$X = list(X = object$X, Y = object$Y) # so that the data is in object$X, either it's a pls or block approach

tests/testthat/test-plotLoadings.R

@@ -59,6 +59,24 @@ test_that("plotLoadings.mint.splsda works", code = {
 
 })
 
+
+test_that("plotLoadings.mint.spls works", code = {
+    data(stemcells)
+    samples <- c(1:5,60:64)
+    X <- stemcells$gene[samples, 1:10]
+    Y <- stemcells$gene[samples+5, 1:10]
+    S <- as.character(stemcells$study[samples])
+
+    res = mint.spls(X = X, Y = Y, ncomp = 3, 
+                    keepX = seq(3, 9, 3), 
+                    keepY = seq(3, 9, 3), 
+                    study = S)
+    pl_res <- plotLoadings(res, contrib = "max")
+
+    expect_is(pl_res, "list")
+})
+
+
 test_that("plotLoadings margin errrors is handled properly", code = {
     data(nutrimouse)
     Y = nutrimouse$diet