minor correction in an example

R/pathwayRes-class.R

@@ -52,8 +52,8 @@ print.pathwayRes <- function(x, ...) {
 #' @importFrom factoextra fviz_pca_ind fviz_eig fviz_pca_var
 #' @examples 
 #' plot(out_test)
-#' plot(out_test, "mmu00052", plot = "var")
-#' plot(out_test, "mmu00052", plot = "ind", habillage = "Age")
+#' plot(out_test, pathway_id = "mmu00052", plot = "var")
+#' plot(out_test, pathway_id = "mmu00052", plot = "ind", habillage = "Age")
 #' @exportS3Method
 plot.pathwayRes <- function(x, ..., pathway_id = NULL, 
                             plot = c("eig", "var", "ind"), habillage = "none") {

man/pathwayRes.Rd

@@ -79,8 +79,8 @@ out_test <- test_pathway(quantif, design, pathways,
 summary(out_test)
 print(out_test)
 plot(out_test)
-plot(out_test, "mmu00052", plot = "var")
-plot(out_test, "mmu00052", plot = "ind", habillage = "Age")
+plot(out_test, pathway_id = "mmu00052", plot = "var")
+plot(out_test, pathway_id = "mmu00052", plot = "ind", habillage = "Age")
 head(out_test)
 extract(out_test, "mmu00562")
 adj_pval <- adjust_pval(out_test)