Java使用Rsession访问远程或本地的Rserve实例！

package com.hessianhealth.common.core.RServe;

import org.math.R.RLogPanel;
import org.math.R.RserverConf;
import org.math.R.Rsession;
import org.rosuda.REngine.REXPMismatchException;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Bean;
import org.springframework.stereotype.Component;

import javax.annotation.PostConstruct;
import java.io.File;
import java.io.IOException;
import java.util.Properties;


/**
 * Created by liangguannan on 2020/9/28.
 * 1.享元模式的主要目的是实现对象的共享，即共享池，当系统中对象多的时候可以减少内存的开销，通常与工厂模式一起使用。
 * 2.Rsession是对Rserve的封装，提供了更高层的API接口，包括Rserve服务器控制，多会话机制
 *
 * http://blog.fens.me/series-r/
 */

/**
 * @Component： 标注Spring管理的Bean，使用@Component注解在一个类上，表示将此类标记为Spring容器中的一个Bean。
 * 当组件不好归类的时候，我们可以使用这个注解进行标注，标识为一个Bean。
 */
@Component
public class RServeHelper {

    private static Rsession rsession=null;

    @Value("${rengine.RUrl}")
    private String url;
    private static String URL;
    @Value("${rengine.RPort}")
    private Integer port;
    private static Integer PORT;

    @PostConstruct
    public void init(){
        URL = url;
        PORT = port;
    }

    /**
     * 利用Rsession初始化RServe
     * 具体Rsession的方法使用可以查看https://github.com/yannrichet/rsession
     * Rsession中的set("...",...)方法的第二个参数为本地数据，一般为现成的数据，只能是本地的数据，如果放入字符串，那么该变量的值就为该字符串。
       如果想要保存一个执行过程中产生的变量，可以使用eval()方法。例如eval("tmp <- head(test)")
     * @return
     * @throws IOException
     */
    @Bean
    private static Rsession initRserve() throws IOException {
        //从配置文件中读取Rserve信息，IP.用户名.密码
/*        RserverConf rconf=new RserverConf(URL,PORT,null,null,new Properties());
        rsession = Rsession.newInstanceTry(System.out, rconf);*/
        return rsession;
    }

    /**
     * 创建Rsession单例
     * @Bean 项目启动时初始化
     * @return
     * @throws IOException
     */
    @Bean
    public static Rsession RsessionInstance() throws IOException {
        if(rsession==null){
            rsession=initRserve();
        }
        return rsession;
    }

    /**
     * 创建Rsession
     * @return
     */
    public static Rsession callRserve(){
        RserverConf rconf = new RserverConf(URL,PORT,null,null,new Properties());
        Rsession s = Rsession.newInstanceTry(System.out, rconf);
        return s;
    }


    /**
     * 测试
         Rsession提供了一种简单的方式，让Java可以访问远程或本地的Rserve实例。Rsession是对Rserve的封装，提供了更高层的API接口，包括Rserve服务器控制，多会话机制，并支持Windows环境。

         接口类
         BusyListener: Notify the state of R engine
         EvalListener: Notify the evaluation of R expression
         Logger: Support R messages printing
         UpdateObjectsListener: Notify the changing of R environment objects
         功能类

         Rdaemon: RServe的守护进程
         RLogPanel: 显示R日志的空间
         RObjectsPanel: 显示R变量的控件
         RserverConf: 连接Rserve实例的配置文件
         Rsession: 连接Rserve实例
         StartRserve: 启动本地的Rserve
     * @param s
     */

    public void test(Rsession s){
        try {
            // 执行R脚本
            double[] rand = s.eval("rnorm(5)").asDoubles();
            System.out.println(rand);

            // 创建一个R对象
            s.set("demo", Math.random());
            s.eval("ls()");

            // 保存R运行时状态到文件
            s.save(new File("./keyan/output/save.Rdata"), "demo");

            // 删除R对象demo
            s.rm("demo");
            s.eval("ls()");

            // 从文件加载R环境
            s.load(new File("./keyan/output/save.Rdata"));
            s.eval("ls()");
            s.eval("print(demo)");

            // 创建一个data.frame对象
            s.set("df", new double[][] { { 1, 2, 3 }, { 4, 5, 6 }, { 7, 8, 9 }, { 10, 11, 12 } }, "x1", "x2", "x3");
            double df$x1_3 = s.eval("df$x1[3]").asDouble();
            System.out.println(df$x1_3);
            s.rm("df");

            //#创建数据框       data.frame  为自带包**
            s.eval("z <- data.frame(sampleId=c('MGJ','MGJ','MGJ2','MGJ2'),subgroup=c('B cells','B cells','B cells, pro','Basophils'),proportion=c(0.0224543895212849,0.115263157894737,0.00272883205987837,0.00447368421052632))");
            s.eval("print(z)");

            // 生成一个图形文件
            s.eval("getwd()");
            s.toJPEG(new File("C:\\Users\\liangguannan\\Desktop\\plot.png"), 400, 400, "plot(rnorm(10))");

            // 以HTML格式输出
            String html = s.asHTML("summary(rnorm(100))");
            System.out.println("------------:"+html);

            // 以文本格式输出
            String txt = s.asString("summary(rnorm(100))");
            System.out.println(txt);

            // 安装新类库
            //System.out.println(s.installPackage("sensitivity", true));
        } catch (REXPMismatchException e) {
            e.printStackTrace();
        }finally {
            s.end();
        }
    }

    /**
     * 分布图测试
     * @param s
     */
    public static void barplot(Rsession s){
        s.eval("library(jsonlite)");
        s.eval("library(ggplot2)");
        s.eval("library(cowplot)");
        s.eval("library(data.table)");

        s.eval("w <- data.table(sampleId=c('MGJ','MGJ','MGJ2','MGJ2'),subgroup=c('B cells','B cells','B cells','Basophils'),proportion=c(0.0224543895212849,0.115263157894737,0.00272883205987837,0.00447368421052632))");
        s.eval("print(w)");

        s.eval("barplotdownload=function(nw,cluster,type,height,base_width,dpi,path)\n" +
                "{\n" +
                "  nw$proportion=round(as.numeric(nw$proportion),digits=3)\n" +
                "  if (type==\"horizontal\")\n" +
                "  {p=ggplot(subset(nw,sampleId%in%cluster),aes(subgroup,proportion,fill=sampleId))+geom_bar(stat=\"identity\",position=\"dodge\")+\n" +
                "    theme_bw()+theme(panel.grid.major=element_line(colour=NA),\n" +
                "                     panel.background = element_rect(fill = \"transparent\",colour = NA),\n" +
                "                     plot.background = element_rect(fill = \"transparent\",colour = NA),\n" +
                "                     panel.grid.minor = element_blank())+\n" +
                "    theme(legend.title = element_blank(), axis.title = element_blank(), axis.text.x = element_text(angle = 45, hjust = 0.5, vjust = 0.5))\n" +
                "  } else {\n" +
                "    p=ggplot(data=subset(nw,sampleId%in%cluster),aes(x=sampleId,y=proportion,fill=subgroup))+geom_col(position=\"fill\")+\n" +
                "      theme_bw()+theme(panel.grid.major=element_line(colour=NA),\n" +
                "                       panel.background = element_rect(fill = \"transparent\",colour = NA),\n" +
                "                       plot.background = element_rect(fill = \"transparent\",colour = NA),\n" +
                "                       panel.grid.minor = element_blank())+\n" +
                "      theme(legend.title = element_blank(),axis.title = element_blank(),\n" +
                "            axis.text.x = element_text(angle = 45, hjust = 0.5, vjust = 0.5))\n" +
                "  }\n" +
                "  \n" +
                "  setwd(path)\n" +
                "  \n" +
                "  save_plot(\"barplot.png\",p,base_height = height, base_width = base_width, dpi=dpi)\n" +
                "  save_plot(\"barplot.pdf\",p,base_height = height, base_width = base_width, dpi=dpi)\n" +
                "}");

        s.eval("barplotdownload(w,c(\"MGJ\",\"MGJ2\"),\"vertical\",10,20,100,\"/home/file\")");
    }

    /**
     * 气泡图测试
     * @param s
     */
    public static void DotPlot(Rsession s){
        //s.load(new File("C:\\Users\\liangguannan\\Desktop\\MGJ_MGJ2_Cluster_all.Rdata"));

        s.eval("library(dplyr)");
        s.eval("library(ggplot2)");
        s.eval("library(cowplot)");

        //s.eval("data.filt=get(load(\"C:\\Users\\liangguannan\\Desktop\\MGJ_MGJ2_Cluster_all.Rdata\"))");

        s.eval("DotPlotdownload=function(datafilt,resolution,genes,cluster,color,height,base_width,dpi,path){\n" +
                "  DefaultAssay(datafilt) <- \"RNA\"\n" +
                "  Idents(data.filt)=resolution\n" +
                "  dotPlot<- DotPlot(data.filt, features=genes,  idents=cluster, cols =  c(\"lightgrey\", color))\n" +
                "  setwd(path)\n" +
                "  save_plot(\"dotplot.png\",dotPlot,base_height = height, base_width = base_width, dpi=dpi)\n" +
                "  save_plot(\"dotplot.pdf\",dotPlot,base_height = height, base_width = base_width, dpi=dpi)\n" +
                "}");

        s.eval("resolution=\"integrated_snn_res.0.8\"");
        s.eval("genes=c(\"Elane\",\"Ctsg\",\"Ibsp\")");
        s.eval("cluster=c(0,1,2,3,5,6)");
        s.eval("color=\"red\"");
        s.eval("path=\"/home/admin\"");

        s.eval("DotPlotdownload(data,resolution,genes,cluster,color,10,20,300,path)");

    }

    /**
     * 散点图
     * @param s
     */
    public static void dimplot(Rsession s){
        s.eval("library(dplyr)");
        s.eval("library(ggplot2)");
        s.eval("library(cowplot)");

        s.eval("datafilt=get(load(\"/home/data/projects/WHBIOBANKS003/result/result.20201119151044/standard_analysis/1_Data_QC_Statistics/Rdata/MGJ_MGJ2_Cluster_all.Rdata\"))");

        s.eval("Dimplotdownload=function(data.filt,resolution,reduction,cluster,split,sizep,sizel,height,base_width,dpi,path)\n" +
                "{\n" +
                "  Idents(data.filt)=resolution\n" +
                "  dim=FetchData(data.filt,vars=resolution,slot=\"data\")\n" +
                "  dim$cell=rownames(dim)\n" +
                "  dimr=dim[which(dim[,resolution] %in% cluster),]\n" +
                "  cell=dimr$cell\n" +
                "  \n" +
                "  setwd(path)\n" +
                "  \n" +
                "  if (split ==FALSE) {\n" +
                "    dimplotall=DimPlot(object = data.filt,cells=cell,reduction = reduction, label = TRUE,\n" +
                "                       pt.size = sizep,label.size = sizel)\n" +
                "    \n" +
                "    \n" +
                "    save_plot(sprintf(\"Dimplotall_%s_.png\", reduction),dimplotall,base_height = height, base_width = base_width, dpi=dpi)\n" +
                "    save_plot(sprintf(\"Dimplotall_%s_.pdf\", reduction),dimplotall,base_height = height, base_width = base_width, dpi=dpi)\n" +
                "  } else {\n" +
                "    dimplotsplit=DimPlot(object = data.filt,cells=cell,reduction = reduction, label = FALSE,\n" +
                "                         pt.size = sizep,label.size = sizel)+facet_wrap(~ident,scales=\"free\")\n" +
                "    \n" +
                "    save_plot(sprintf(\"Dimplotsplit_%s_.png\", reduction),dimplotsplit,base_height = height, base_width = base_width, dpi=dpi)\n" +
                "    save_plot(sprintf(\"Dimplotsplit_%s_.pdf\", reduction),dimplotsplit,base_height = height, base_width = base_width, dpi=dpi)}\n" +
                "  \n" +
                "}");


        s.eval("resolution=\"integrated_snn_res.0.8\"");
        s.eval("genes=c(\"Elane\",\"Ctsg\",\"Ibsp\")");
        s.eval("cluster=c(0,1,2,3,5,6)");
        s.eval("path=\"/home/admin\"");
        s.eval("reduction=\"tsne\"");
        s.eval("split=FALSE");
        s.eval("sizep=1");
        s.eval("sizel=6");

        s.eval("Dimplotdownload(datafilt,resolution,reduction,cluster,split,sizep,sizel,10,20,300,path)");
    }

    /**
     * 小提琴图
     * @param s
     */
    public static void vlnPlot(Rsession s){
        s.eval("library(dplyr)");

        s.eval("VlnPlotdownload=function(datafilt,genes,cluster,base_height,base_width,dpi,path)\n" +
                "{\n" +
                "  Idents(datafilt)=resolution\n" +
                "  dim=FetchData(data.filt,vars=resolution,slot=\"data\")\n" +
                "  dim$cell=rownames(dim)\n" +
                "  dimr=dim[which(dim[,resolution] %in% cluster),]\n" +
                "  cell=dimr$cell\n" +
                "  \n" +
                "  modify_vlnplot <- function(obj, feature, pt.size = 0, plot.margin = unit(c(-0.75, 0, -0.75, 0), \"cm\"),...) {\n" +
                "    p <- VlnPlot(obj, features = feature, pt.size = pt.size, ... ) +\n" +
                "      xlab(\"\") + ylab(feature) + ggtitle(\"\") +\n" +
                "      theme(legend.position = \"none\",\n" +
                "            axis.text.x = element_blank(),\n" +
                "            axis.text.y = element_blank(),\n" +
                "            axis.ticks.x = element_blank(),\n" +
                "            axis.ticks.y = element_line(),\n" +
                "            axis.title.y = element_text(size = rel(1), angle = 0, vjust = 0.5),\n" +
                "            plot.margin = plot.margin )\n" +
                "    return(p)\n" +
                "  }\n" +
                "  \n" +
                "  ## main function\n" +
                "  StackedVlnPlot <- function(obj, features, pt.size = 0, plot.margin = unit(c(-0.75, 0, -0.75, 0), \"cm\"), ...) {\n" +
                "    plot_list <- purrr::map(features, function(x) modify_vlnplot(obj = obj,feature = x, ...))\n" +
                "    plot_list[[length(plot_list)]]<- plot_list[[length(plot_list)]] +\n" +
                "      theme(axis.text.x=element_text(), axis.ticks.x = element_line())\n" +
                "    p <- patchwork::wrap_plots(plotlist = plot_list, ncol = 1)\n" +
                "    return(p)\n" +
                "  }\n" +
                "  \n" +
                "  DefaultAssay(datafilt) <- \"RNA\"\n" +
                "  \n" +
                "  data2=datafilt[,cell]\n" +
                "  plot=StackedVlnPlot(data2, genes, pt.size=0)\n" +
                "  \n" +
                "  setwd(path)\n" +
                "  \n" +
                "  save_plot(\"StackedVlnPlot.png\", plot, base_height = base_height,base_width =  base_width, dpi=dpi)\n" +
                "  save_plot(\"StackedVlnPlot.pdf\", plot, base_height = base_height,base_width =  base_width, dpi=dpi)\n" +
                "}");

        s.eval("resolution=\"integrated_snn_res.0.8\"");
        s.eval("genes=c(\"Elane\",\"Ctsg\",\"Ibsp\")");
        s.eval("cluster=c(0,1,2,3,5,6)");
        s.eval("color=\"red\"");
        s.eval("path=\"/home/admin\"");

        s.eval("VlnPlotdownload(datafilt,resolution,genes,cluster,10,20,300,path)");
    }

    /**
     * 热力图
     * @param s
     */
    public static void Heatmap(Rsession s){
        s.eval("library(SCVIS)");
        s.eval("datafilt=get(load(\"/home/data/projects/WHBIOBANKS003/result/result.20201119151044/standard_analysis/1_Data_QC_Statistics/Rdata/MGJ_MGJ2_Cluster_all.Rdata\"))");

        s.eval("resolution=\"integrated_snn_res.0.8\"");
        s.eval("cluster=c(0,1,2,3,5,6)");
        s.eval("genes=c(\"Elane\",\"Ctsg\",\"Ibsp\")");
        s.eval("path=\"/home/keyan/reportPDF\"");

        s.eval("Heatmapdownload(datafilt,resolution,cluster,genes,8,16,300,path)");

    }

    /**
     * @param args
     */
    public static void main(String[] args) {
        RserverConf rconf = new RserverConf("192.168.8.144", 6311, "conan", "conan", new Properties());
        Rsession s = Rsession.newInstanceTry(System.out, rconf);

        try {

            //s.eval("help(package=\"SCVIS\")");
            Heatmap(s);


            System.exit(0);//避免JDWP Unable to get JNI 1.2 environment
        } catch (Exception e) {
            e.printStackTrace();
        }finally {
            s.close();
        }


    }
}