Version 1.04

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: LMSstat
 Title: AUTOMATION OF STATISTICAL TESTS WITH AN IDENTICAL DATA INPUT.
-Version: 1.0.3
+Version: 1.0.4
 Authors@R: 
     person(given = "CHANG-HO",
            family = "KIM",

R/AS_barplot.R

@@ -16,10 +16,10 @@
 #' @return ggbarplot
 #' @export
 #'
-#' @examples D<-as.data.frame(cbind(LETTERS,rep(1,26),c(rep("A",7),rep("B",6),rep("C",13)),runif(26),runif(26)))
-#' Datas<-rbind(c("Sample","Multilevel","Group","some metabolite1","some metabolite2"),D)
-#' Test<-Allstats(Datas)
-#' AS_barplot(Test,asterisk = "Dunn",significant_variable_only = F,color = c("#FF3300","#FF6600","#FFCC00","#99CC00","#0066CC","#660099") )
+#' @example data(Data)
+#' Test<-Allstats(Data)
+#' AS_barplot(Test,asterisk = "Dunn",significant_variable_only = F,color = c("#FF3300","#FF6600","#FFCC00","#99CC00","#0066CC","#660099"))
+#'
 AS_barplot<-function(data,
                      asterisk="t_test",
                      significant_variable_only=F,

R/AS_boxplot.R

@@ -16,9 +16,8 @@
 #' @return ggboxplot
 #' @export
 #'
-#' @examples D<-as.data.frame(cbind(LETTERS,rep(1,26),c(rep("A",7),rep("B",6),rep("C",13)),runif(26),runif(26)))
-#' Datas<-rbind(c("Sample","Multilevel","Group","some metabolite1","some metabolite2"),D)
-#' Test<-Allstats(Datas)
+#' @examples data(Data)
+#' Test<-Allstats(Data)
 #' AS_boxplot(Test,asterisk = "Dunn",significant_variable_only = F,color = c("#FF3300","#FF6600","#FFCC00","#99CC00","#0066CC","#660099") )
 AS_boxplot<-function(data,
                      asterisk="t_test",

R/AS_dotplot.R

@@ -16,9 +16,8 @@
 #' @return ggdotplot
 #' @export
 #'
-#' @examples D<-as.data.frame(cbind(LETTERS,rep(1,26),c(rep("A",7),rep("B",6),rep("C",13)),runif(26),runif(26)))
-#' Datas<-rbind(c("Sample","Multilevel","Group","some metabolite1","some metabolite2"),D)
-#' Test<-Allstats(Datas)
+#' @examples data(Data)
+#' Test<-Allstats(Data)
 #' AS_dotplot(Test,asterisk = "Dunn",significant_variable_only = F,color = c("#FF3300","#FF6600","#FFCC00","#99CC00","#0066CC","#660099") )
 AS_dotplot<-function(data,
                      asterisk="t_test",

R/Allstats.R

@@ -7,9 +7,8 @@
 #' @return List including Result Matrix of p-values, converted datas.
 #' @export
 #'
-#' @examples D<-as.data.frame(cbind(LETTERS,rep(1,26),c(rep("A",7),rep("B",6),rep("C",13)),runif(26),runif(26)))
-#' Datas<-rbind(c("Sample","Multilevel","Group","some metabolite1","some metabolite2"),D)
-#' Allstats(Datas)
+#' @examples data(Data)
+#' Result<-Allstats(Data)
 #'
 #'
 Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")

R/NMDS.R

@@ -0,0 +1,66 @@
+#' Automatically save NMDS plots for the selected dimension metrics
+#'
+#' @param Data 
+#' @param methods #methods<- c("manhattan", "euclidean", "canberra", "clark", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn",  "raup", "binomial", "mahalanobis", "chisq","chord") #can be any distance c["manhattan", "euclidean", "canberra", "clark", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial", "chao", "cao", "mahalanobis", "chisq","chord"]
+#' @param color colors used for ggplots.color=c("#FF3300","#FF6600","#FFCC00","#99CC00","#0066CC","#660099")
+#' @param legend_position legend position "none","left","right","bottom","top"
+#' @param fig_width figure size
+#' @param fig_height figure size
+#'
+#' @return NMDS plot
+#' @export
+#'
+#' @examples data(Data) 
+#' NMDS(Data,methods = c("euclidian","manhattan","bray"))
+
+NMDS<-function(Data,
+               methods=c("euclidean","bray"),
+               color = c("#FF3300","#660099","#FFCC00","#99CC00","#0066CC","#FF6600"),
+               legend_position = "bottom",
+               fig_width = 24,
+               fig_height = 20
+               ){
+  ifelse(!dir.exists(file.path(getwd(), "NMDS")), dir.create(file.path(getwd(), "NMDS")), FALSE)
+  colnames(Data) <- Data[1, ]
+  Data <- Data[-1, -2]
+  Data<-Data %>% dplyr::arrange(Group)
+  rownames(Data)<-Data[,1];Data<-Data[,-1]
+  Data[,2:ncol(Data)]<-sapply(Data[,2:ncol(Data)],function(x) as.numeric(x))
+  NMDS_Data_input<-Data#subset samples of interest, columns: Group(Male, Female etc)+metabolite, rownames : sample names
+  NMDS_Data_input[,1]<-as.factor(NMDS_Data_input[,1]) # Group as factors
+  for(method in methods){
+  Dist_Met<-as.matrix(vegan::vegdist(NMDS_Data_input[,2:ncol(NMDS_Data_input)],method = method))
+  NMDS=vegan::metaMDS(Dist_Met,k = 2,trymax = 2000)#Bray curtis
+  x_y_coord<-as.data.frame(vegan::scores(NMDS,display = "sites"))
+  x_y_coord_G <- cbind(x_y_coord, NMDS_Data_input$Group)
+  colnames(x_y_coord_G)[3]<-"Group"
+  M_p_value<-vegan::adonis2(Dist_Met~Group,
+                     method = method,
+                     by = NULL,
+                     data = x_y_coord_G)[["Pr(>F)"]][1] #Model P_Value
+  ggplot2::ggplot() +
+    ggplot2::geom_point(data = x_y_coord_G, ggplot2::aes(x = NMDS1, y = NMDS2, 
+                                       color = Group), size = 3)+ 
+    ggplot2::theme_minimal() +
+    ggplot2::scale_color_manual(values = color)+
+    ggplot2::theme(plot.title=ggplot2::element_text(size=10,
+                                                    face="bold",
+                                                    color="Black",
+                                                    hjust=0.5,
+                                                    lineheight=1.2),  # title
+                   plot.subtitle=ggplot2::element_text(size=15,
+                                                       hjust=0.5),  # subtitle
+                   plot.caption=ggplot2::element_text(size=15),  # caption
+                   axis.title.x=ggplot2::element_text(vjust=0,
+                                                      size=10),  # X axis title
+                   axis.title.y=ggplot2::element_text(size=10),  # Y axis title
+                   legend.position = legend_position)+
+    ggplot2::stat_ellipse(ggplot2::aes(x=x_y_coord_G$NMDS1,
+                                       y=x_y_coord_G$NMDS2,color=x_y_coord_G$Group),
+                          type = "norm")+
+    ggplot2::ggtitle(paste(method,"index/distance, ","Stress Level : ",NMDS$stress,"Model_p_value",M_p_value))
+  ggplot2::ggsave(paste(method,"NMDS.png",sep = "_"),
+                  path=paste0(getwd(),"/NMDS"),
+                  height = fig_height,
+                  width = fig_width,units = "cm")
+  }}

man/NEWS.Rd

@@ -28,3 +28,8 @@
     \item AS_dotplot Optimization for paper ready figures
   }
 }
+\section{Changes in version 1.0.4,(July 2021)}{
+  \itemize{
+  \item NMDS added
+  }
+}