corrections

NAMESPACE

@@ -3,9 +3,14 @@
 S3method(adjust_pval,pathwayRes)
 S3method(extract,pathwayRes)
 S3method(head,pathwayRes)
+S3method(plot,MFApath)
 S3method(plot,PCApath)
 S3method(plot,pathwayRes)
+S3method(print,MFApath)
+S3method(print,PCApath)
 S3method(print,pathwayRes)
+S3method(summary,MFApath)
+S3method(summary,PCApath)
 S3method(summary,pathwayRes)
 export(adjust_pval)
 export(extract)

R/pathwayRes-class.R

@@ -28,10 +28,23 @@ summary.pathwayRes <- function(object, ...) {
   cat("Tested effects:", object[[1]]$test_pathway$Fixed_effect)
 }
 
+#' @exportS3Method 
+summary.PCApath <- function(object, ...) {
+  cat("phoenics method based on PCA\n")
+  NextMethod()
+}
+
+#' @exportS3Method 
+summary.MFApath <- function(object, ...) {
+  cat("phoenics method based on MFA\n")
+  NextMethod()
+}
+
 #' @rdname pathwayRes
 #' @aliases print.pathwayRes
 #' @examples 
 #' print(out_test)
+#' print(out_test2)
 #' @exportS3Method 
 print.pathwayRes <- function(x, ...) {
   cat("A list of pathways which contains for each pathway: \n")
@@ -39,10 +52,21 @@ print.pathwayRes <- function(x, ...) {
   cat("$", names(path_res)[1], ": ", "Pathway name \n", sep = "")
   cat("$", names(path_res)[2], ": ", "Pathway code \n", sep = "")
   cat("$", names(path_res)[3], ": ", "Metabolites in the pathway \n", sep = "")
-  cat("$", names(path_res)[4], ": ", "PCA results \n", sep = "")
+  cat("$", names(path_res)[4], ": ", "Factor analysis results \n", sep = "")
   cat("$", names(path_res)[5], ": ", "Model results \n", sep = "")
   cat("$", names(path_res)[6], ": ", "Pathway test results \n", sep = "")
-  cat("$", names(path_res)[7], ": ", "Type of factor analysis \n", sep = "")
+}
+
+#' @exportS3Method 
+print.PCApath <- function(x, ...) {
+  cat("phoenics method based on PCA\n")
+  NextMethod()
+}
+
+#' @exportS3Method 
+print.MFApath <- function(x, ...) {
+  cat("phoenics method based on MFA\n")
+  NextMethod()
 }
 
 #' @rdname pathwayRes
@@ -97,43 +121,54 @@ plot.PCApath <- function(x, ..., pathway_id = NULL,
   
   object_sub <- extract.pathwayRes(x, pathway_id)
   
-  analysis <- object_sub[[1]]$analysis
+  if (plot == "var") {
+    p <- factoextra::fviz_pca_var(object_sub[[1]]$PCA,
+                                  title = object_sub[[1]]$pathway_name,
+                                  repel = TRUE)
+    return(p)
+  }
+  if (plot == "ind") {
+    p <- factoextra::fviz_pca_ind(object_sub[[1]]$PCA, habillage = habillage,
+                                  title = object_sub[[1]]$pathway_name,
+                                  geom = "point", pointsize = 2,
+                                  mean.point = FALSE)
+    return(p)
+  }
+  NextMethod()
+}
+
+#' @exportS3Method
+plot.MFApath <- function(x, ..., pathway_id = NULL, 
+                         plot = c("eig", "var", "ind", "group"),
+                         habillage = "none") {
+  
+  plot <- match.arg(plot)
   
-  if (analysis == "PCA") {
-    if (plot == "var") {
-      p <- factoextra::fviz_pca_var(object_sub[[1]]$PCA,
-                                    title = object_sub[[1]]$pathway_name,
-                                    repel = TRUE)
-      return(p)
-    }
-    if (plot == "ind") {
-      p <- factoextra::fviz_pca_ind(object_sub[[1]]$PCA, habillage = habillage,
-                                    title = object_sub[[1]]$pathway_name,
-                                    geom = "point", pointsize = 2,
-                                    mean.point = FALSE)
-      return(p)
-    }
+  if (is.null(pathway_id)) {
+    message("`pathway_id` not specified... defaulting to the first pathway")
+    pathway_id <- names(x)[1]
   }
-  if (analysis == "MFA") {
-    if (plot == "group") {
-      p <- factoextra::fviz_mfa_var(object_sub[[1]]$PCA, choice = "group",
-                                    title = object_sub[[1]]$pathway_name,
-                                    repel = TRUE)
-      return(p)
-    }
-    if (plot == "var") {
-      p <- factoextra::fviz_mfa_var(object_sub[[1]]$PCA, choice = "quanti.var",
-                                    title = object_sub[[1]]$pathway_name,
-                                    repel = TRUE)
-      return(p)
-    }
-    if (plot == "ind") {
-      p <- factoextra::fviz_mfa_ind(object_sub[[1]]$PCA, partial = "all",
-                                    habillage = habillage,
-                                    title = object_sub[[1]]$pathway_name,
-                                    pointsize = 2)
-      return(p)
-    }
+  
+  object_sub <- extract.pathwayRes(x, pathway_id)
+  
+  if (plot == "group") {
+    p <- factoextra::fviz_mfa_var(object_sub[[1]]$PCA, choice = "group",
+                                  title = object_sub[[1]]$pathway_name,
+                                  repel = TRUE)
+    return(p)
+  }
+  if (plot == "var") {
+    p <- factoextra::fviz_mfa_var(object_sub[[1]]$PCA, choice = "quanti.var",
+                                  title = object_sub[[1]]$pathway_name,
+                                  repel = TRUE)
+    return(p)
+  }
+  if (plot == "ind") {
+    p <- factoextra::fviz_mfa_ind(object_sub[[1]]$PCA, partial = "all",
+                                  habillage = habillage,
+                                  title = object_sub[[1]]$pathway_name,
+                                  pointsize = 2)
+    return(p)
   }
   NextMethod()
 }
@@ -170,10 +205,11 @@ extract <- function(object, pathway_id) {
 
 #' @exportS3Method
 extract.pathwayRes <- function(object, pathway_id) {
+  class_sub <- class(object)
   cond <- lapply(object, function(path) path$pathway_code %in% pathway_id |
                    path$pathway_name %in% pathway_id)
   object_sub <- object[unlist(cond)]
-  class(object_sub) <- c("PCApath", "pathwayRes")
+  class(object_sub) <- class_sub
   return(object_sub)
 }
 

R/test_pathway.R

@@ -35,9 +35,9 @@
 #' @param analysis character string indicating if the pathway scores are
 #' obtained using \link[FactoMineR]{PCA} or \link[FactoMineR]{MFA}
 #' 
-#' @return an object of class \code{PCApath} and \code{pathwayRes} which is a 
-#' list of pathway results. Each element of the list contain the following
-#' entries:
+#' @return an object of class \code{PCApath} or \code{MFApath} and 
+#' \code{pathwayRes} which is a list of pathway results. Each element of the 
+#' list contain the following entries:
 #' \item{pathway_name}{a character corresponding to the pathway name}
 #' \item{pathway_code}{a character corresponding to the pathway code}
 #' \item{metabolites}{a data.frame with the names and codes of the quantified
@@ -48,7 +48,6 @@
 #' \item{model}{the output of the mixed model fit}
 #' \item{test_pathway}{a data.frame with the p-values for each tested fixed
 #' effect}
-#' \item{analysis}{a character corresponding to the parameter \code{analysis}}
 #' 
 #' @importFrom FactoMineR PCA MFA
 #' @importFrom lme4 lmer
@@ -308,13 +307,18 @@ test_pathway <- function(quantif, design, pathways = "auto", fixed, random,
     
     res <- list("pathway_name" = path_name, "pathway_code" = path_code,
                 "metabolites" = out_met, "PCA" = res_pca, "model" = res_lmm,
-                "test_pathway" = res_test, "analysis" = analysis)
+                "test_pathway" = res_test)
     
     return(res)
   })
   
   names(res_pathway) <- unique(pathways$pathway_name)
-  class(res_pathway) <- c("PCApath", "pathwayRes")
+  if (analysis == "PCA") {
+    class(res_pathway) <- c("PCApath", "pathwayRes")
+  }
+  if (analysis == "MFA") {
+    class(res_pathway) <- c("MFApath", "pathwayRes")
+  }
   
   return(res_pathway)
 }

man/pathwayRes.Rd

@@ -82,6 +82,7 @@ out_test2 <- test_pathway(quantif, design, pathways,
                          npc = 2, model = "blmer", analysis = "MFA")
 summary(out_test2)
 print(out_test)
+print(out_test2)
 plot(out_test)
 plot(out_test, pathway_id = "mmu00052", plot = "var")
 plot(out_test, pathway_id = "mmu00052", plot = "ind", habillage = "Age")

man/test_pathway.Rd

@@ -59,9 +59,9 @@ using \link[lme4]{lmer} or \link[blme]{blmer}. Default to \code{"lmer"}}
 obtained using \link[FactoMineR]{PCA} or \link[FactoMineR]{MFA}}
 }
 \value{
-an object of class \code{PCApath} and \code{pathwayRes} which is a 
-list of pathway results. Each element of the list contain the following
-entries:
+an object of class \code{PCApath} or \code{MFApath} and 
+\code{pathwayRes} which is a list of pathway results. Each element of the 
+list contain the following entries:
 \item{pathway_name}{a character corresponding to the pathway name}
 \item{pathway_code}{a character corresponding to the pathway code}
 \item{metabolites}{a data.frame with the names and codes of the quantified
@@ -72,7 +72,6 @@ from \link[FactoMineR]{MFA})}
 \item{model}{the output of the mixed model fit}
 \item{test_pathway}{a data.frame with the p-values for each tested fixed
 effect}
-\item{analysis}{a character corresponding to the parameter \code{analysis}}
 }
 \description{
 Perform a differential analysis at pathway level based on