Merge pull request #180 from mixOmicsTeam/issue-120

Fix for Issue #120
mixOmicsTeam · May 2, 2022 · d18f41c · d18f41c
2 parents ceebc84 + 9512ea4
commit d18f41c
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Showing 2 changed files with 21 additions and 6 deletions.
diff --git a/R/plotLoadings.R b/R/plotLoadings.R
@@ -176,6 +176,8 @@ plotLoadings.mixo_pls <-
         if (length(block) == 1 & !is.null(name.var))
             name.var = list(name.var = name.var)
 
+        contrib.df <- list()
+
         for (i in 1 : length(block))
         {
             res = get.loadings.ndisplay(object = object, comp = comp, block = block[i], name.var = name.var[[i]], name.var.complete = name.var.complete, ndisplay = ndisplay)
@@ -204,8 +206,12 @@ plotLoadings.mixo_pls <-
             } else if (length(block) > 1 & !missing(subtitle)) {
                 title(paste(subtitle[i]), line=0, cex.main = size.subtitle)
             }
+
+            contrib.df <- c(contrib.df, list(df))
         }
 
+        names(contrib.df) <- block
+
         if (length(block) > 1 & !is.null(title))
             title(title, outer=TRUE, line = -2, cex.main = size.title)
 
@@ -215,7 +221,7 @@ plotLoadings.mixo_pls <-
         par(mar = omar) #reset mar
 
         # return the contribution matrix
-        return(invisible(df))
+        return(invisible(contrib.df))
     }
 
 #' @rdname plotLoadings
@@ -391,6 +397,9 @@ plotLoadings.mixo_plsda <-
             if (length(block) == 1 & !is.null(name.var))
                 name.var = list(name.var = name.var)
 
+
+            contrib.df <- list()
+
             for (i in 1 : length(block))
             {
                 res = get.loadings.ndisplay(object = object, comp = comp, block = block[i], name.var = name.var[[i]], name.var.complete = name.var.complete, ndisplay = ndisplay)
@@ -457,9 +466,14 @@ plotLoadings.mixo_plsda <-
                                title = paste(legend.title),
                                cex = size.legend)
                     }
+
+                    contrib.df <- c(contrib.df, list(df))
                 } # end if plot
             }
 
+            names(contrib.df) <- block
+
+
             if(plot) # overall title and reset par if needed
             {
                 # legend
@@ -473,7 +487,7 @@ plotLoadings.mixo_plsda <-
             }
 
             # return the contribution matrix
-            return(invisible(df))
+            return(invisible(contrib.df)) # df
         }# end contrib missing
     }
 
@@ -1253,6 +1267,7 @@ get.contrib.df <- function(Y,
         method.group[[k]] = tapply(X[, k], Y, method, na.rm=TRUE) #method is either mean or median
         # determine which group has the highest mean/median
         which.contrib[k, 1:nlevels(Y)] = (method.group[[k]]) == get(contrib)((method.group[[k]]), na.rm=TRUE) # contrib is either min or max
+
     }
 
     # we also add an output column indicating the group that is max

diff --git a/tests/testthat/test-plotLoadings.R b/tests/testthat/test-plotLoadings.R
@@ -10,7 +10,7 @@ test_that("plotLoadings.spls works", code = {
 
     pl_res <- plotLoadings(toxicity.spls)
 
-    expect_is(pl_res, "data.frame")
+    expect_is(pl_res, "list")
 
 })
 
@@ -23,7 +23,7 @@ test_that("plotLoadings.splsda works", code = {
 
     pl_res <- plotLoadings(splsda.liver, comp = 1, method = 'median')
 
-    expect_is(pl_res, "data.frame")
+    expect_is(pl_res, "list")
 
 })
 
@@ -42,7 +42,7 @@ test_that("plotLoadings.block.splsda works", code = {
 
     pl_res <- plotLoadings(nutrimouse.sgccda,block=2)
 
-    expect_is(pl_res, "data.frame")
+    expect_is(pl_res, "list")
 
 })
 
@@ -55,7 +55,7 @@ test_that("plotLoadings.mint.splsda works", code = {
     res = mint.splsda(X = data, Y = type.id, ncomp = 3, keepX = c(10,5,15), study = exp)
     pl_res <- plotLoadings(res, contrib = "max")
 
-    expect_is(pl_res, "data.frame")
+    expect_is(pl_res, "list")
 
 })