{"id":30158,"date":"2024-02-28T18:02:16","date_gmt":"2024-02-28T10:02:16","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30158"},"modified":"2024-02-28T18:02:18","modified_gmt":"2024-02-28T10:02:18","slug":"%e9%87%8d%e7%a3%85%e6%9d%a5%e8%a2%ad%ef%bc%8c%e5%8f%aa%e9%9c%805%e5%88%86%e9%92%9f%e5%ae%8c%e5%85%a8%e6%8e%8c%e6%8f%a1%e5%8d%95%e7%bb%86%e8%83%9e%e5%a4%9a%e6%a0%b7%e6%9c%ac%e7%bb%86%e8%83%9e%e4%ba%92","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30158","title":{"rendered":"\u91cd\u78c5\u6765\u88ad\uff0c\u53ea\u97005\u5206\u949f\u5b8c\u5168\u638c\u63e1\u5355\u7ec6\u80de\u591a\u6837\u672c\u7ec6\u80de\u4e92\u4f5c\u5206\u6790"},"content":{"rendered":"

\u91cd\u78c5\u6765\u88ad\uff0c\u53ea\u97005\u5206\u949f\u5b8c\u5168\u638c\u63e1\u5355\u7ec6\u80de\u591a\u6837\u672c\u7ec6\u80de\u4e92\u4f5c\u5206\u6790<\/p>\n

\u5728\u4e0a\u4e00\u671f\u6211\u4eec\u8fdb\u884c\u4e86\u5355\u7ec6\u80de\u5355\u6837\u672c\u7ec6\u80de\u4e92\u4f5c\u5206\u6790\uff0c\uff0c\u6211\u4eec\u4e3a\u4f55\u8981\u505a\u5355\u7ec6\u80de\u4e92\u4f5c\u5206\u6790\uff1f\u8bb8\u591a\u751f\u7269\u8fdb\u7a0b\u548c\u7ec6\u80de\u901a\u8baf\u606f\u606f\u76f8\u5173\uff0c\u6bd4\u5982\u5668\u5b98\u5f62\u6210\uff0c\u80da\u80ce\u53d1\u80b2\uff0c\u764c\u75c7\u53d1\u751f\u53d1\u5c55\uff0c\u708e\u75c7\u53cd\u5e94\uff0c\u836f\u7269\u4f5c\u7528\u548c\u8010\u836f\u7814\u7a76\u7b49\uff1b\u8be5\u5206\u6790\u5728\u5355\u7ec6\u80de\u5206\u6790\u4e2d\u5177\u6709\u5f88\u9ad8\u7684\u91cd\u8981\u6027\uff0c\u8be5\u5206\u6790\u5c5e\u4e8e\u5355\u7ec6\u80de\u5206\u6790\u4e2d\u7684\u9ad8\u7ea7\u5206\u6790\u5185\u5bb9\uff0c\u5728\u6587\u7ae0\u4e2d\u6dfb\u52a0\u8be5\u5206\u6790\u4f1a\u4f7f\u4f60\u7684\u6587\u7ae0\u589e\u8272\u4e0d\u5c11\uff0c\u4eca\u5929\u5c0f\u679c\u60f3\u5c1d\u8bd5\u591a\u6837\u672c\u7ec6\u80de\u4e92\u4f5c\u5206\u6790\uff0c\u8fd8\u662f\u5229\u7528CellChat \u5305\u8fdb\u884c\u5206\u6790\uff0c\u6559\u7a0b\u53ef\u4ee5\u53c2\u8003\u5b98\u7f51(https:\/\/htmlpreview.github.io\/?https:\/\/github.com\/sqjin\/CellChat\/blob\/master\/tutorial\/Comparison_analysis_of_multiple_datasets.html),\u5982\u679c\u89c9\u5f97\u63a8\u6587\u4e0d\u9519\uff0c\u70b9\u8d5e\u52a0\u5173\u6ce8\u5965\uff0c\u8bdd\u4e0d\u591a\u8bf4\u5f00\u59cb\u4eca\u5929\u7684\u5206\u4eab\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

    \n
  1. \u5b89\u88c5\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n

    library(devtools)<\/p>\n

    devtools::install_github(“sqjin\/CellChat”)<\/p>\n

    install.packages(“magrittr”)<\/p>\n

    install.packages(\u201cpatchwork\u201d)<\/p>\n

    install.packages(\u201ctidyverse\u201d)<\/p>\n

    BioCmanager::install(\u201cSeurat\u201d)<\/p>\n

      \n
    1. \u5bfc\u5165\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n

      library(CellChat)<\/p>\n

      library(patchwork)<\/p>\n

      library(magtittr)<\/p>\n

      library(tidyverse)<\/p>\n

      library(Seurat)<\/p>\n

        \n
      1. \u8bfb\u53d6\u793a\u4f8b\u6570\u636e<\/li>\n<\/ol>\n

        #\u8be5\u6570\u636e\u4e3a\u524d\u671f\u4fdd\u5b58\u7684\u5355\u7ec6\u80de\u6570\u636e\u5206\u6790\u7ed3\u679c<\/p>\n

        immune.combined<- readRDS(“immune.combined.rds”)<\/p>\n

          \n
        1. Chellchat\u591a\u6837\u672c\u5206\u6790<\/li>\n<\/ol>\n

          ## STIM\u7ec4\u6837\u672cchellchat\u5206\u6790<\/p>\n

          stim.object <- subset(immune.combined,stim==”STIM”)<\/p>\n

          stim.data.input <- GetAssayData(stim.object, assay = “RNA”, slot = “data”)<\/p>\n

          stim.meta <- stim.object@meta.data[,c(“seurat_annotations”, “stim”)]<\/p>\n

          stim.meta$CellType %<>% as.vector(.)<\/p>\n

          #\u521b\u5efaCellChat\u5bf9\u8c61<\/p>\n

          stim.cellchat <- createCellChat(object = stim.data.input)<\/p>\n

          stim.cellchat <- addMeta(stim.cellchat, meta = stim.meta)<\/p>\n

          stim.cellchat <- setIdent(stim.cellchat, ident.use = “seurat_annotations”)<\/p>\n

          cellchat <- createCellChat(object = data.input, meta = meta, group.by = “labels”)<\/p>\n

          # CellChat\u63d0\u4f9b\u7684\u4eba\u7684\u914d\u53d7\u4f53\u6570\u636e\u5e93<\/p>\n

          stim.cellchat@DB <- CellChatDB.human<\/p>\n

          stim.cellchat <- subsetData(stim.cellchat)<\/p>\n

          #\u4f7f\u7528\u591a\u7ebf\u7a0b\u8fdb\u884c\u8ba1\u7b97<\/p>\n

          future::plan(“multisession”, workers = 10)<\/p>\n

          #\u7528\u4e8e\u7ec6\u80de-\u7ec6\u80de\u901a\u4fe1\u5206\u6790\u7684\u8868\u8fbe\u6570\u636e\u9884\u5904\u7406<\/p>\n

          stim.cellchat <- identifyOverExpressedGenes(stim.cellchat)<\/p>\n

          stim.cellchat <- identifyOverExpressedInteractions(stim.cellchat)<\/p>\n

          stim.cellchat <- projectData(stim.cellchat, PPI.human)<\/p>\n

          #\u5728\u4fe1\u53f7\u901a\u8def\u6c34\u5e73\u63a8\u65ad\u7ec6\u80de\u95f4\u901a\u4fe1<\/p>\n

          stim.cellchat <- computeCommunProb(stim.cellchat)<\/p>\n

          #\u8ba1\u7b97\u805a\u5408\u7684\u7ec6\u80de\u95f4\u7684\u901a\u4fe1\u7f51\u7edc<\/p>\n

          stim.cellchat <- aggregateNet(stim.cellchat)<\/p>\n

          #\u4fdd\u5b58cellchat\u5206\u6790\u7ed3\u679c<\/p>\n

          saveRDS(stim.cellchat,”stim.cellchat.rds”)<\/p>\n

          ## CTRL\u7ec4\u6837\u672cCellchat\u5206\u6790<\/p>\n

          ctrl.object <- subset(immune.combined,stim==”CTRL”)<\/p>\n

          ctrl.data.input <- GetAssayData(ctrl.object, assay = “RNA”, slot = “data”)<\/p>\n

          ctrl.meta = ctrl.object@meta.data[,c(“seurat_annotations”, “stim”)]<\/p>\n

          ctrl.meta$CellType %<>% as.vector(.)<\/p>\n

          ctrl.cellchat <- createCellChat(object = ctrl.data.input)<\/p>\n

          ctrl.cellchat <- addMeta(ctrl.cellchat, meta = ctrl.meta)<\/p>\n

          ctrl.cellchat <- setIdent(ctrl.cellchat, ident.use = “seurat_annotations”)<\/p>\n

          ctrl.cellchat@DB <- CellChatDB.human<\/p>\n

          ctrl.cellchat <- subsetData(ctrl.cellchat)<\/p>\n

          future::plan(“multisession”, workers = 10)<\/p>\n

          #\u7528\u4e8e\u7ec6\u80de-\u7ec6\u80de\u901a\u4fe1\u5206\u6790\u7684\u8868\u8fbe\u6570\u636e\u9884\u5904\u7406<\/p>\n

          ctrl.cellchat <- identifyOverExpressedGenes(ctrl.cellchat)<\/p>\n

          ctrl.cellchat <- identifyOverExpressedInteractions(ctrl.cellchat)<\/p>\n

          ctrl.cellchat <- projectData(ctrl.cellchat, PPI.human)<\/p>\n

          ctrl.cellchat <- computeCommunProb(ctrl.cellchat)<\/p>\n

          ctrl.cellchat <- computeCommunProbPathway(ctrl.cellchat)<\/p>\n

          #\u8ba1\u7b97\u805a\u5408\u7684\u7ec6\u80de\u95f4\u7684\u901a\u4fe1\u7f51\u7edc<\/p>\n

          ctrl.cellchat <- aggregateNet(ctrl.cellchat)<\/p>\n

          #\u4fdd\u5b58cellchat\u5206\u6790\u7ed3\u679c<\/p>\n

          saveRDS(ctrl.cellchat,”ctrl.cellchat.rds”)<\/p>\n

            \n
          1. \u52a0\u8f7d\u4e24\u4e2a\u6570\u636e\u96c6\u7684Cellchat\u5bf9\u8c61\uff0c\u7136\u540e\u5408\u5e76\u5728\u4e00\u8d77<\/li>\n<\/ol>\n

            object.list <- list(CTRL = ctrl.cellchat, STIM = stim.cellchat)<\/p>\n

            cellchat <- mergeCellChat(object.list, add.names = names(object.list))<\/p>\n

              \n
            1. \u8fdb\u884c\u4e92\u4f5c\u6b21\u6570\u548c\u4e92\u4f5c\u5f3a\u5ea6\u5206\u6790<\/li>\n<\/ol>\n

              gg1 <- compareInteractions(cellchat, show.legend = F, group = c(1,2))<\/p>\n

              gg2 <- compareInteractions(cellchat, show.legend = F, group = c(1,2), measure = “weight”)<\/p>\n

              pdf(“compareInteractions.pdf”,height = 5,width = 8)<\/p>\n

              gg1 + gg2<\/p>\n

              dev.off()<\/p>\n

              \"Dingtalk_20230315155331\"<\/p>\n

              \u6ce8\uff1a\u4e24\u4e2a\u5206\u7ec4\u7684\u4e92\u4f5c\u6b21\u6570\u548c\u4e92\u4f5c\u5f3a\u5ea6\u67f1\u72b6\u56fe<\/p>\n

                \n
              1. \u4e0d\u540c\u7ec6\u80de\u7fa4\u76f8\u4e92\u4f5c\u7528\u6b21\u6570\u548c\u4f5c\u7528\u5f3a\u5ea6\u5dee\u5f02<\/li>\n<\/ol>\n

                #\u7f51\u7edc\u56fe\u7ed8\u5236<\/p>\n

                pdf(“netVisual_diffInteraction.pdf”,height = 10,width = 10)<\/p>\n

                par(mfrow = c(1,2), xpd=TRUE)<\/p>\n

                netVisual_diffInteraction(cellchat, weight.scale = T)<\/p>\n

                netVisual_diffInteraction(cellchat, weight.scale = T, measure = “weight”)<\/p>\n

                dev.off()<\/p>\n

                \"Dingtalk_20230315160409\"<\/p>\n

                #\u70ed\u56fe\u7ed8\u5236<\/p>\n

                gg1 <- netVisual_heatmap(cellchat)<\/p>\n

                gg2 <- netVisual_heatmap(cellchat, measure = “weight”)<\/p>\n

                pdf(“netVisual_heatmap.pdf”,height = 5,width = 8)<\/p>\n

                gg1 + gg2<\/p>\n

                dev.off()<\/p>\n

                \"Dingtalk_20230315160712\"<\/p>\n

                #\u4e0d\u540c\u6570\u636e\u96c6\u7684\u4e92\u4f5c\u7f51\u7edc\u56fe<\/p>\n

                pdf(“netVisual_diffInteraction.pdf”,height = 10,width = 10)<\/p>\n

                weight.max <- getMaxWeight(object.list, attribute = c(“idents”,”count”))<\/p>\n

                par(mfrow = c(1,2), xpd=TRUE)<\/p>\n

                for (i in 1:length(object.list)) {<\/p>\n

                netVisual_circle(object.list[[i]]@net$count, weight.scale = T, label.edge= F, edge.weight.max = weight.max[2], edge.width.max = 12, title.name = paste0(“Number of interactions – “, names(object.list)[i]))<\/p>\n

                }<\/p>\n

                dev.off()<\/p>\n

                \"Dingtalk_20230315161140\"<\/p>\n

                #\u8bc6\u522b\u4e0a\u8c03\u548c\u4e0b\u8c03\u7684\u53d7\u4f53-\u914d\u4f53\u5bf9<\/p>\n

                pdf(“netVisual_bubble.pdf”,height = 10,width = 10)<\/p>\n

                netVisual_bubble(cellchat, sources.use = 4, targets.use = c(5:11), comparison = c(1, 2), angle.x = 45)<\/p>\n

                dev.off()<\/p>\n

                \"Dingtalk_20230315161904\"<\/p>\n

                \u4eca\u5929\u5c0f\u679c\u5bf9\u5355\u7ec6\u80de\u591a\u6837\u672c\u7ec6\u80de\u4e92\u4f5c\u5206\u6790\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u5e72\u8d27\u6ee1\u6ee1\u5965\uff0c\u6709\u9700\u8981\u7684\u53ef\u4ee5\u501f\u9274\u5b66\u4e60\u5965\uff0c\u8fdb\u884c\u8be5\u5206\u6790\u9700\u8981\u719f\u7ec3\u638c\u63e1\u5355\u7ec6\u80de\u5206\u6790\u6d41\u7a0b\uff0c\u5355\u7ec6\u80de\u76f8\u5173\u5206\u6790\u5185\u5bb9\u53ef\u4ee5\u5c1d\u8bd5\u4f7f\u7528\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u4e91\u5e73\u53f0\u751f\u7269\u4fe1\u606f\u5206\u6790\u5c0f\u5de5\u5177\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html\uff0c\u5305\u62ec\u5355\u7ec6\u80de\u5206\u6790(http:\/\/www.biocloudservice.com\/366\/366.php),\u5355\u7ec6\u80de\u6570\u636e\u7ed8\u5236\u5c0f\u63d0\u7434\u56fe(http:\/\/www.biocloudservice.com\/788\/788.php),\u7ed8\u5236\u5355\u7ec6\u80detSNE\u56fe(http:\/\/www.biocloudservice.com\/229\/229.php)\u7b49\u5355\u7ec6\u80de\u5206\u6790\u76f8\u5173\u5c0f\u5de5\u5177\uff0c\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u6b22\u8fce\u5c0f\u4f19\u4f34\u548c\u5c0f\u679c\u4e00\u8d77\u8ba8\u8bba\u5b66\u4e60\u5965\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

                \u91cd\u78c5\u6765\u88ad\uff0c\u53ea\u97005\u5206\u949f\u5b8c\u5168\u638c\u63e1\u5355\u7ec6\u80de\u591a\u6837\u672c\u7ec6\u80de\u4e92\u4f5c\u5206\u6790 \u5728\u4e0a\u4e00\u671f\u6211\u4eec\u8fdb\u884c\u4e86\u5355\u7ec6\u80de\u5355\u6837\u672c\u7ec6\u80de\u4e92\u4f5c\u5206\u6790\uff0c\uff0c\u6211\u4eec\u4e3a\u4f55\u8981 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30158"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=30158"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30158\/revisions"}],"predecessor-version":[{"id":30164,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30158\/revisions\/30164"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=30158"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=30158"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=30158"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}