covid_comp_shiny.R

+makeFig1 <- function(df){
+  
+  # prepare data for colors etc
+  colMethods <- c("deepskyblue4", "darkorange" , "deepskyblue3" , "mediumseagreen" , "yellow3" , "black")
+  nameMethods <- c("BUSTED", "BppM1M2", "BppM7M8", "codemlM1M2", "codemlM7M8", "MEME")
+  metColor <- data.frame(Name = nameMethods , Col = colMethods , stringsAsFactors = FALSE)
+  
+  # subset for this specific figure
+  #df <- df[df$nbY >= 1, ] # to drop genes found by 0 methods (big datasets)
+  xt <- df[, c("BUSTED", "BppM1M2", "BppM7M8", "codemlM1M2", "codemlM7M8")]
+  xt$Gene <- df$Gene
+  nbrMeth <- 5
+  # reverse order of dataframe so that genes with the most Y are at the bottom (to be on top of the barplot)
+  xt[,1:5] <- ifelse(xt[,1:5] == "Y", 1, 0)
+  # sort and Filter the 0 lines
+  xt<-xt[order(rowSums(xt[,1:5])),]
+  xt<-na.omit(xt[rowSums(xt[,1:5])>2,])  
+  
+  row.names(xt)<-xt$Gene
+  xt<-xt[,1:5]
+  
+  colFig1 <- metColor[which(metColor$Name %in% colnames(xt)) , ]
+  
+  ##### PART 1 : NUMBER OF METHODS
+  par(xpd = NA , mar=c(2,7,4,0) ,   oma = c(0,0,0,0) , mgp = c(3,0.3,0))
+  
+  h =  barplot(
+    t(xt),
+    border = NA ,
+    axes = F ,
+    col = adjustcolor(colFig1$Col, alpha.f = 1),
+    horiz = T ,
+    las  = 2 ,
+    main = "Methods detecting positive selection" , 
+    cex.main = 0.85,
+    cex.names  = min(50/nrow(xt), 1.5)
+  )
+  
+  axis(3, line = 0, at = c(0:nbrMeth), label = c("0", rep("", nbrMeth -1), nbrMeth), tck = 0.02)
+  
+  legend("bottomleft",
+         horiz = T,
+         border = colFig1$Col,
+         legend = colFig1$Name, 
+         fill = colFig1$Col,
+         cex = 0.8,
+         bty = "n",
+         xpd = NA
+  )
+}
+
+
+df<-read.delim(paste0(workdir,
+                      "/data/DGINN_202005281649summary_cleaned.csv"), 
+               fill=T, h=T, sep=",")
+