Version 1.09

Volcano plot

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: LMSstat
 Title: AUTOMATION OF STATISTICAL TESTS WITH AN IDENTICAL DATA INPUT.
-Version: 1.0.8
+Version: 1.0.9
 Authors@R: 
     person(given = "CHANG-HO",
            family = "KIM",

NAMESPACE

@@ -12,6 +12,7 @@ export(NMDS)
 export(Norm_test)
 export(PCA)
 export(PCoA)
+export(Volcano)
 export(aroc_compute)
 export(data_summary)
 export(roc_all)

R/Volcano.R

@@ -0,0 +1,160 @@
+#' Volcano plot for every group comparison
+#'
+#' @param data data inheriting from Allstats
+#' @param asterisk statistics inheriting from Allstats # "t-test", "u-test", "Scheffe", "Dunn"
+#' @param reverse reverse the direction of fold change
+#' @param fig_width figure size
+#' @param FC_log Fold change log transformation value
+#' @param pval_log p_value log transformation value
+#' @param fig_height figure size
+#' @param dotsize dotsize
+#' @param x_limit x axis limt c( -3,3)
+#' @param y_limit y axis limit c(0, 100)
+#' @param pval_intercept intercept for identification 0.05
+#' @param sig_label label significant variables
+#' @param color colors used for ggplots.color=c("#FF3300","#FF6600","#FFCC00","#99CC00","#0066CC","#660099")
+#'
+#' @return Volcano Plot
+#' @export
+#'
+#' @examples data(Data)
+#' Test<-Allstats(Data)
+#' Volcano(Test,asterisk = "t-test")
+
+Volcano<-function(data,
+                  asterisk = "t-test",
+                  reverse = F,
+                  fig_width = NA,
+                  FC_log = 2,
+                  pval_log = 10,
+                  fig_height = NA,
+                  dotsize=2,
+                  x_limit = c(-15,15),
+                  y_limit = c(-2,6),
+                  pval_intercept = 0.05,
+                  sig_label = T,
+                  color = c("blue","black", "red")){
+  ifelse(!dir.exists(file.path(getwd(), "Volcano")), dir.create(file.path(getwd(), "Volcano")), FALSE)
+  data[["Data_renamed"]]<-data[["Data_renamed"]] %>% plyr::mutate(
+    ZZZZ =data[["Data_renamed"]][,2] )
+  data[["Data_renamed"]]<-data[["Data_renamed"]][,c(-1,-2)]
+  data[["Data_renamed"]][,1:(ncol(data[["Data_renamed"]])-1)]<-sapply(data[["Data_renamed"]][,1:(ncol(data[["Data_renamed"]])-1)],
+                                                                      function(x) as.numeric(x))
+  NAMES<-colnames(data[["Data"]][3:ncol(data[["Data"]])])
+  data[["Data_renamed"]]$ZZZZ<-as.factor(data[["Data_renamed"]]$ZZZZ)
+  Comb<-gtools::combinations(length(unique(data[["Data"]]$Group)),2,unique(data[["Data"]]$Group))
+
+  {if (asterisk =="Scheffe"){
+      p_val_data<-data[["Anova_PostHoc"]]}
+  else if (asterisk =="t-test"){
+    p_val_data<-data[["t_test"]]}
+  else if (asterisk =="u-test"){
+    p_val_data<-data[["u_test"]]}
+  else if (asterisk =="Dunn"){
+    p_val_data<-data[["Dunn"]]}
+  else {
+    print("Wrong asterisk input must be one of (Dunn,Scheffe,u_test,t_test)")}}
+
+  {if(length(unique(data[["Data"]]$Group)) !=2){
+    for(a in 1:nrow(p_val_data)){
+      for(b in 1:ncol(p_val_data)){
+        if(is.nan(p_val_data[a,b])==T){
+          p_val_data[a,b]<-1
+        }
+      }
+    }}
+  else if(length(unique(data[["Data"]]$Group))==2){
+    for(b in 1:length(p_val_data)){
+      if(is.nan(p_val_data[b])==T){
+        p_val_data[b]<-1
+      }
+    }
+  }}
+
+  for (a in 1: nrow(Comb)){
+    {if(reverse ==T){
+      G1<- Comb[a,2]
+      G2<- Comb[a,1]
+    }
+      else if (reverse ==F){
+        G1<- Comb[a,1]
+        G2<- Comb[a,2]
+      }
+  data[["Data"]][,3:ncol(data[["Data"]])]<-apply(data[["Data"]][,3:ncol(data[["Data"]])],2,function(x)as.numeric(x))
+  Part_dat_1<-data[["Data"]] %>% dplyr::filter(Group == G1)
+  Part_dat_2<-data[["Data"]] %>% dplyr::filter(Group == G2)
+  Volc_Dat<-matrix(nrow = (ncol(data[["Data"]])-2),ncol = 3)
+  }
+  for (i in 3:ncol(Part_dat_1)){
+    Volc_Dat[(i-2),1]<- log(mean(Part_dat_1[,i])/mean(Part_dat_2[,i]),base = FC_log) }
+    if(length(unique(data[["Data"]]$Group))>2)
+  {if(asterisk == "Scheffe"){
+    {if (paste0(Comb[a,1],"-",Comb[a,2],"___","ANO_posthoc")%in% colnames(p_val_data)==T){
+      part_p_val<-p_val_data[,paste0(Comb[a,1],"-",Comb[a,2],"___","ANO_posthoc")]
+    }
+      else {part_p_val<-p_val_data[,paste0(Comb[a,2],"-",Comb[a,1],"___","ANO_posthoc")]}}
+  }
+  else if(asterisk == "Dunn"){
+    {if (paste0(Comb[a,1]," - ",Comb[a,2],"___","Kru_posthoc(Dunn)")%in% colnames(p_val_data)==T){
+      part_p_val<-p_val_data[,paste0(Comb[a,1]," - ",Comb[a,2],"___","Kru_posthoc(Dunn)")]
+    }
+      else {part_p_val<-p_val_data[,paste0(Comb[a,2]," - ",Comb[a,1],"___","Kru_posthoc(Dunn)")]}}
+  }
+  else{
+    {if (paste0(Comb[a,1],"-",Comb[a,2],"___",asterisk)%in% colnames(p_val_data)==T){
+      part_p_val<-p_val_data[,paste0(Comb[a,1],"-",Comb[a,2],"___",asterisk)]
+    }
+      else {part_p_val<-p_val_data[,paste0(Comb[a,2],"-",Comb[a,1],"___",asterisk)]}}
+
+  }}
+  else  if(length(unique(data[["Data"]]$Group))==2){
+    {part_p_val<-p_val_data}
+  }
+
+  Volc_Dat[,2]<-part_p_val
+  rownames(Volc_Dat)<-colnames(data[["Data"]])[3:ncol(data[["Data"]])]
+  Volc_Dat<-as.data.frame(Volc_Dat)
+  colnames(Volc_Dat)<-c("log2FoldChange","pvalue","Direction")
+  Volc_Dat$Direction <- "Not Significant"
+  Volc_Dat$Direction[Volc_Dat$log2FoldChange > 0 & Volc_Dat$pvalue < pval_intercept] <- "UP"
+  Volc_Dat$Direction[Volc_Dat$log2FoldChange < 0 & Volc_Dat$pvalue < pval_intercept] <- "DOWN"
+  KK<-Volc_Dat %>% dplyr::filter(Direction!="Not Significant")
+    sem_res<-ggplot2::ggplot(data=Volc_Dat, ggplot2::aes(x=log2FoldChange, y=-log(pvalue,base = pval_log), col=Direction)) +
+      ggplot2::geom_point(size= dotsize) +
+      ggplot2::labs(title=paste0(G1," divided by ",G2," Volcano plot"),
+                    x =eval(parse(text = paste0("expression(Log[",FC_log,"]~(Fold~Change))"))),
+                    y = eval(parse(text = paste0("expression(Log[",pval_log,"]~(P-value))"))))+
+      ggplot2::theme_classic()+ ggplot2::theme(plot.title=ggplot2::element_text(size=25,
+                                                     color="Black",
+                                                     hjust=0.5,
+                                                     lineheight=1.2),  # title
+                             plot.subtitle=ggplot2::element_text(size=15,
+                                                        hjust=0.5),  # subtitle
+                             plot.caption=ggplot2::element_text(size=15),  # caption
+                             axis.title.x=ggplot2::element_text(vjust=0,
+                                                       size=15),  # X axis title
+                             axis.title.y=ggplot2::element_text(size=15),  # Y axis title
+                             axis.text.x=ggplot2::element_text(size=10,
+                                                      vjust=.5),  # X axis text
+                             axis.text.y=ggplot2::element_text(size=10))+
+      ggplot2::scale_color_manual(values=color[c("DOWN","Not Significant","UP")%in% unique(Volc_Dat$Direction)]) +
+      ggplot2::geom_vline(xintercept=c(0), col=c("black")) +
+      ggplot2::geom_hline(yintercept=-log(pval_intercept,base = pval_log), col="black")+
+      ggplot2::xlim(x_limit[1], x_limit[2])+
+      ggplot2::ylim(y_limit[1],y_limit[2])
+
+     {if (sig_label== T){
+      sem_res<- sem_res+ggrepel::geom_text_repel(size=3,
+                                        ggplot2::aes(label =ifelse(Volc_Dat$Direction!="Not Significant",
+                                                                   rownames(Volc_Dat),"")))
+      sem_res
+     }
+     else {sem_res}}
+
+    ggplot2::ggsave(filename = paste(G1, "divided by", G2, "Volcano plot.png",collapse = ""),
+                    path=paste0(getwd(),"/Volcano"),
+                    width = fig_width,
+                    height = fig_height)
+
+  }
+}

man/LMSstat-package.Rd

@@ -29,13 +29,15 @@ The package includes
 * PCA
 
 * PCoA
+
+* Volcano
 }
 \details{
 \tabular{ll}{
 Package: \tab LMSstat\cr
 Type: \tab Package\cr
-Version: \tab 1.0.8\cr
-Date: \tab 2021-07-29\cr
+Version: \tab 1.0.9\cr
+Date: \tab 2021-08-02\cr
 License: \tab MIT License\cr
 }
 }

man/NEWS.Rd

@@ -1,6 +1,6 @@
 \name{NEWS}
 \alias{NEWS}
-\title{News for Package
+\title{News for Package}
 
 \section{Changes in version 1.0.1,(February 2021)}{
   \itemize{
@@ -55,3 +55,9 @@
   \item PCoA added
   }
 }
+\section{Changes in version 1.0.9,(August 2021)}{
+  \itemize{
+  \item Volcano plot added
+  }
+}
+