R在剧情上等效

Question

我正在尝试将绘图的代码从基础R转换为利用UNION DISTINCT库。这是绘图的代码，以及图像。 plotly是一个正在读入的表（在此处的代码上方），其中包含不同GSE＃的组之间的对比。 （有关详细信息，请参阅here）

contrastTable

除了情节明显的间距/缩放问题外，我还有两个主要问题。

1）如何在#Get gene to plot gene = toupper(readline(prompt="Enter gene name (e.g. GZMA): ")) #Find all instances of query gene in master contrast table geneLines = grep(paste("^",gene,"$",sep = ""),contrastTable[,"gene"]) #If the gene is found at least once, continue if (length(geneLines)>0) { ########Plot contrasts par(oma = c(1,10,1,1)) geneRows = contrastTable[geneLines,] fcs = as.list(geneRows$logFC) names(fcs) = paste(geneRows$GSE,"\n",geneRows$Group2," \U2192 ",geneRows$Group1,sep = "") maxFC = max(as.numeric(as.character(geneRows$logFC))) minFC = min(as.numeric(as.character(geneRows$logFC))) #Set up marker color and type markers = rep(4,length(fcs)) markers[which(as.numeric(as.character(geneRows[,"adj.P.Val"]))<0.05)] = 15 markers[which(as.numeric(as.character(geneRows[,"adj.P.Val"]))<0.01)] = 19 outerCol = rep("grey20",length(fcs)) outerCol[which(as.numeric(as.character(geneRows[,"adj.P.Val"]))<0.05)] = "darkorange" outerCol[which(as.numeric(as.character(geneRows[,"adj.P.Val"]))<0.01)] = "red" layout(t(c(1,2)), c(3.5,1), c(1,1)) #Plot all contrasts stripchart(fcs,xlim = c(min(-2,minFC),max(2,maxFC)),las = 1,col = outerCol,pch = markers,main = gene,xlab = expression(paste("log"[2],"(Fold Change)")),cex.axis=0.75) abline(v = 0,col = "grey50",lty=2) abline(v = log(c(0.5,2/3,1.5,2),2),col = "grey80",lty=2) usr = par("usr") legend(usr[1]-(usr[2]-usr[1])/3.5,usr[3]-(usr[4]-usr[3])/10,c("p \u2265 0.05","p < 0.05","p < 0.01"),col = c("black","darkorange","red"),pch = c(4,15,19),cex = 0.7,xpd = TRUE) #add confidence interval for (i in 1:nrow(geneRows)) { segments(geneRows[i,"CI.L"],i,geneRows[i,"CI.R"],i,col = "grey50") } #Re-plot to put markers on top par(new=TRUE) stripchart(fcs,xlim = c(min(-2,minFC),max(2,maxFC)),las = 1,col = outerCol,pch = markers,xlab = "",ylab = "",xaxt = "n",yaxt="n") #add lines dividing different GSE#s datasetList = geneRows$GSE hLines =(which(duplicated(datasetList) == FALSE) - 0.5) abline(h = hLines, col = "grey80") 中重新创建每个GSE＃之间的水平线？ （现在目前由最后两行代码完成）

2）如何在plotly中重新显示y轴，它显示GSE＃，在下面显示plotly种格式？

非常感谢任何帮助！