Merge pull request #339 from mixOmicsTeam/issue-336

Issue 336
mixOmicsTeam · Nov 11, 2024 · 9ee3c22 · 9ee3c22
2 parents 3d13a76 + 1bcd7f1
commit 9ee3c22
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Showing 49 changed files with 133 additions and 294 deletions.
diff --git a/R/block.pls.R b/R/block.pls.R
@@ -24,7 +24,8 @@
 #' Four PLS algorithms are available: PLS regression \code{("regression")}, PLS
 #' canonical analysis \code{("canonical")}, redundancy analysis
 #' \code{("invariant")} and the classical PLS algorithm \code{("classic")} (see
-#' References and \code{?pls} for more details).
+#' References and \code{?pls} for more details). Note that the argument 'scheme' 
+#' has now been hardcoded to 'horst' and 'init' to 'svd.single'. 
 #' 
 #' Note that our method is partly based on Generalised Canonical Correlation
 #' Analysis and differs from the MB-PLS approaches proposed by Kowalski et al.,
@@ -50,11 +51,6 @@
 #'   off-diagonal elements of a fully connected design (see examples in
 #'   \code{block.splsda}). If \code{Y} is provided instead of \code{indY}, the
 #'   \code{design} matrix is changed to include relationships to \code{Y}.
-#' @param scheme Character, one of 'horst', 'factorial' or 'centroid'. Default =
-#' \code{'horst'}, see reference.
-#' @param init Mode of initialization use in the algorithm, either by Singular
-#' Value Decomposition of the product of each block of X with Y ('svd') or each
-#' block independently ('svd.single'). Default = \code{svd.single}
 #' @template arg/verbose.call
 #' @return \code{block.pls} returns an object of class \code{'block.pls'}, a
 #' list that contains the following components:
@@ -95,10 +91,8 @@ block.pls <- function(X,
                       indY,
                       ncomp = 2,
                       design,
-                      scheme,
                       mode,
                       scale = TRUE,
-                      init ,
                       tol = 1e-06,
                       max.iter = 100,
                       near.zero.var = FALSE,
@@ -108,8 +102,8 @@ block.pls <- function(X,
 
     # call to 'internal_wrapper.mint.block'
     result = internal_wrapper.mint.block(X=X, Y=Y, indY=indY, ncomp=ncomp,
-                                         design=design, scheme=scheme, mode=mode, scale=scale,
-                                         init=init, tol=tol, max.iter=max.iter ,near.zero.var=near.zero.var,
+                                         design=design, scheme="horst", mode=mode, scale=scale,
+                                         init="svd.single", tol=tol, max.iter=max.iter ,near.zero.var=near.zero.var,
                                          all.outputs = all.outputs, DA = FALSE)
 
     # calculate weights for each dataset

diff --git a/R/block.plsda.R b/R/block.plsda.R
@@ -54,6 +54,7 @@
 #' \item{call}{if \code{verbose.call = FALSE}, then just the function call is returned.
 #' If \code{verbose.call = TRUE} then all the inputted values are accessable via
 #' this component}
+#' Note that the argument 'scheme' has now been hardcoded to 'horst' and 'init' to 'svd.single'. 
 #' @author Florian Rohart, Benoit Gautier, Kim-Anh Lê Cao, Al J Abadi
 #' @seealso \code{\link{plotIndiv}}, \code{\link{plotArrow}},
 #' \code{\link{plotLoadings}}, \code{\link{plotVar}}, \code{\link{predict}},
@@ -95,9 +96,7 @@ block.plsda <- function(X,
                         indY,
                         ncomp = 2,
                         design,
-                        scheme,
                         scale = TRUE,
-                        init = "svd",
                         tol = 1e-06,
                         max.iter = 100,
                         near.zero.var = FALSE,
@@ -151,10 +150,10 @@ block.plsda <- function(X,
         indY = indY,
         ncomp = ncomp,
         design = design,
-        scheme = scheme,
+        scheme = "horst",
         mode = 'regression',
         scale = scale,
-        init = init,
+        init = "svd.single",
         tol = tol,
         max.iter = max.iter,
         near.zero.var = near.zero.var,

diff --git a/R/block.spls.R b/R/block.spls.R
@@ -70,6 +70,7 @@
 #' \item{call}{if \code{verbose.call = FALSE}, then just the function call is returned.
 #' If \code{verbose.call = TRUE} then all the inputted values are accessable via
 #' this component}
+#' Note that the argument 'scheme' has now been hardcoded to 'horst' and 'init' to 'svd.single'. 
 #' @author Florian Rohart, Benoit Gautier, Kim-Anh Lê Cao, Al J Abadi
 #' @seealso \code{\link{plotIndiv}}, \code{\link{plotArrow}},
 #' \code{\link{plotLoadings}}, \code{\link{plotVar}}, \code{\link{predict}},
@@ -98,10 +99,8 @@ block.spls = function(X,
                       keepX,
                       keepY,
                       design,
-                      scheme,
                       mode,
                       scale = TRUE,
-                      init ,
                       tol = 1e-06,
                       max.iter = 100,
                       near.zero.var = FALSE,
@@ -118,10 +117,10 @@ block.spls = function(X,
         keepX = keepX,
         keepY = keepY,
         design = design,
-        scheme = scheme,
+        scheme = "horst",
         mode = mode,
         scale = scale,
-        init = init,
+        init = "svd.single",
         tol = tol,
         max.iter = max.iter,
         near.zero.var = near.zero.var,

diff --git a/R/block.splsda.R b/R/block.splsda.R
@@ -56,6 +56,7 @@
 #' \item{call}{if \code{verbose.call = FALSE}, then just the function call is returned.
 #' If \code{verbose.call = TRUE} then all the inputted values are accessable via
 #' this component}
+#' Note that the argument 'scheme' has now been hardcoded to 'horst' and 'init' to 'svd.single'. 
 #' @author Florian Rohart, Benoit Gautier, Kim-Anh Lê Cao, Al J Abadi
 #' @seealso \code{\link{plotIndiv}}, \code{\link{plotArrow}},
 #' \code{\link{plotLoadings}}, \code{\link{plotVar}}, \code{\link{predict}},
@@ -95,9 +96,7 @@ block.splsda <- function(X,
                          ncomp = 2,
                          keepX,
                          design,
-                         scheme,
                          scale = TRUE,
-                         init = "svd",
                          tol = 1e-06,
                          max.iter = 100,
                          near.zero.var = FALSE,
@@ -154,10 +153,10 @@ block.splsda <- function(X,
         keepX = keepX,
         DA = TRUE,
         design = design,
-        scheme = scheme,
+        scheme = 'horst',
         mode = 'regression',
         scale = scale,
-        init = init,
+        init = 'svd.single',
         tol = tol,
         max.iter = max.iter,
         near.zero.var = near.zero.var,

diff --git a/R/mint.block.pls.R b/R/mint.block.pls.R
@@ -54,6 +54,7 @@
 #' subsequent S3 methods} \item{max.iter}{the maximum number of iterations,
 #' used for subsequent S3 methods} \item{iter}{Number of iterations of the
 #' algorithm for each component}
+#' Note that the argument 'scheme' has now been hardcoded to 'horst' and 'init' to 'svd.single'. 
 #' @author Florian Rohart, Benoit Gautier, Kim-Anh Lê Cao, Al J Abadi
 #' @seealso \code{\link{spls}}, \code{\link{summary}}, \code{\link{plotIndiv}},
 #' \code{\link{plotVar}}, \code{\link{predict}}, \code{\link{perf}},
@@ -101,10 +102,8 @@ mint.block.pls <- function(X,
                            study,
                            ncomp = 2,
                            design,
-                           scheme,
                            mode,
                            scale = TRUE,
-                           init ,
                            tol = 1e-06,
                            max.iter = 100,
                            near.zero.var = FALSE,
@@ -118,10 +117,10 @@ mint.block.pls <- function(X,
         study = study,
         ncomp = ncomp,
         design = design,
-        scheme = scheme,
+        scheme = 'horst',
         mode = mode,
         scale = scale,
-        init = init,
+        init = 'svd.single',
         tol = tol,
         max.iter = max.iter,
         near.zero.var = near.zero.var,

diff --git a/R/mint.block.plsda.R b/R/mint.block.plsda.R
@@ -76,6 +76,7 @@
 #' subsequent S3 methods} \item{max.iter}{the maximum number of iterations,
 #' used for subsequent S3 methods} \item{iter}{Number of iterations of the
 #' algorithm for each component}
+#' Note that the argument 'scheme' has now been hardcoded to 'horst' and 'init' to 'svd.single'. 
 #' @author Florian Rohart, Benoit Gautier, Kim-Anh Lê Cao, Al J Abadi
 #' @seealso \code{\link{spls}}, \code{\link{summary}}, \code{\link{plotIndiv}},
 #' \code{\link{plotVar}}, \code{\link{predict}}, \code{\link{perf}},
@@ -137,9 +138,7 @@ mint.block.plsda <- function(X,
                              study,
                              ncomp = 2,
                              design,
-                             scheme,
                              scale = TRUE,
-                             init ,
                              tol = 1e-06,
                              max.iter = 100,
                              near.zero.var = FALSE,
@@ -189,10 +188,10 @@ mint.block.plsda <- function(X,
         study = study,
         ncomp = ncomp,
         design = design,
-        scheme = scheme,
+        scheme = 'horst',
         mode = 'regression',
         scale = scale,
-        init = init,
+        init = 'svd.single',
         tol = tol,
         max.iter = max.iter,
         near.zero.var = near.zero.var,

diff --git a/R/mint.block.spls.R b/R/mint.block.spls.R
@@ -46,6 +46,7 @@
 #' subsequent S3 methods} \item{max.iter}{the maximum number of iterations,
 #' used for subsequent S3 methods} \item{iter}{Number of iterations of the
 #' algorithm for each component}
+#' Note that the argument 'scheme' has now been hardcoded to 'horst' and 'init' to 'svd.single'. 
 #' @author Florian Rohart, Benoit Gautier, Kim-Anh Lê Cao, Al J Abadi
 #' @seealso \code{\link{spls}}, \code{\link{summary}}, \code{\link{plotIndiv}},
 #' \code{\link{plotVar}}, \code{\link{predict}}, \code{\link{perf}},
@@ -95,10 +96,8 @@ mint.block.spls <- function(X,
                             keepX,
                             keepY,
                             design,
-                            scheme,
                             mode,
                             scale = TRUE,
-                            init ,
                             tol = 1e-06,
                             max.iter = 100,
                             near.zero.var = FALSE,
@@ -114,10 +113,10 @@ mint.block.spls <- function(X,
         keepX = keepX,
         keepY = keepY,
         design = design,
-        scheme = scheme,
+        scheme = 'horst',
         mode = mode,
         scale = scale,
-        init = init,
+        init = 'svd.single',
         tol = tol,
         max.iter = max.iter,
         near.zero.var = near.zero.var,

diff --git a/R/mint.block.splsda.R b/R/mint.block.splsda.R
@@ -48,6 +48,7 @@
 #' subsequent S3 methods} \item{max.iter}{the maximum number of iterations,
 #' used for subsequent S3 methods} \item{iter}{Number of iterations of the
 #' algorithm for each component}
+#' Note that the argument 'scheme' has now been hardcoded to 'horst' and 'init' to 'svd.single'. 
 #' @author Florian Rohart, Benoit Gautier, Kim-Anh Lê Cao, Al J Abadi
 #' @seealso \code{\link{spls}}, \code{\link{summary}}, \code{\link{plotIndiv}},
 #' \code{\link{plotVar}}, \code{\link{predict}}, \code{\link{perf}},
@@ -111,9 +112,7 @@ mint.block.splsda <- function(X,
                               ncomp = 2,
                               keepX,
                               design,
-                              scheme,
                               scale = TRUE,
-                              init ,
                               tol = 1e-06,
                               max.iter = 100,
                               near.zero.var = FALSE,
@@ -162,10 +161,10 @@ mint.block.splsda <- function(X,
         ncomp = ncomp,
         keepX = keepX,
         design = design,
-        scheme = scheme,
+        scheme = 'horst',
         mode = 'regression',
         scale = scale,
-        init = init,
+        init = 'svd.single',
         tol = tol,
         max.iter = max.iter,
         near.zero.var = near.zero.var,