{"id":28854,"date":"2024-02-19T17:53:45","date_gmt":"2024-02-19T09:53:45","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=28854"},"modified":"2024-02-19T17:53:46","modified_gmt":"2024-02-19T09:53:46","slug":"%e5%88%86%e7%b1%bb%e5%8f%98%e9%87%8f%e7%83%ad%e5%9b%be%e7%bb%98%e5%88%b6","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=28854","title":{"rendered":"\u5206\u7c7b\u53d8\u91cf\u70ed\u56fe\u7ed8\u5236"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u7ed8\u5236\u4e00\u4e0b\u5206\u7c7b\u53d8\u91cf\u53d8\u91cf\u70ed\u56fe\uff0c\u7ed8\u5236\u8be5\u56fe\u9700\u8981\u4e09\u4e2a\u8f93\u5165\u6587\u4ef6\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

    \n
  1. \u5b89\u88c5\u6240\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n

    BiocManager::install(\u201cComplexHeatmap\u201d)<\/p>\n

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

      library(ComplexHeatmap)<\/p>\n

        \n
      1. \u5bfc\u5165\u6570\u636e<\/li>\n<\/ol>\n

        #\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u4e2d\u7684logFC<\/p>\n

        logfc <- read.csv(“logFc.csv”, row.names = 1)<\/p>\n

        \"Dingtalk_20230129155507\"<\/p>\n

        #\u5dee\u5f02\u5206\u6790\u4e2d\u7684P\u503c<\/p>\n

        p.val <- read.csv(“PVal.csv”, row.names = 1)<\/p>\n

        \"Dingtalk_20230129155918\"<\/p>\n

        #\u57fa\u56e0\u5206\u7ec4<\/p>\n

        genetype <- read.csv(“genetype.csv”)<\/p>\n

        \"Dingtalk_20230129160103\"<\/p>\n

        3.\u4ee3\u7801\u5c55\u793a<\/p>\n

        #\u4e3a\u786e\u4fdd\u70ed\u56fe\u57fa\u56e0\u7684\u987a\u5e8f\u548c\u5206\u7ec4\u6587\u4ef6\u7684\u987a\u5e8f\u662f\u4e00\u81f4\u7684<\/p>\n

        #\u56e0\u6b64\u6309\u7167\u57fa\u56e0\u5206\u7ec4\u6587\u4ef6\u91cc\u7684\u987a\u5e8f\uff0c\u5bf9logfc\u548cp.val\u4e24\u4e2a\u6587\u4ef6\u6392\u5e8f<\/p>\n

        logfcOrdered <- logfc[genetype$gene,]<\/p>\n

        p.valOrdered <- p.val[genetype$gene,]<\/p>\n

        ## \u5bf9logfc\u8fdb\u884c\u5206\u7c7b<\/p>\n

        logfcCat <- apply(logfcOrdered, 2, function(x){<\/p>\n

        cut(x, breaks = c(-Inf, -2, -1, 1, 2, Inf),<\/p>\n

        labels = c(“< -2”, “-2 – -1”, “-1 – 1”, “1 – 2”, “> 2”))<\/p>\n

        })<\/p>\n

        rownames(logfcCat) <- rownames(logfcOrdered)<\/p>\n

        ## \u786e\u4fdd\u4e24\u4e2a\u6570\u636e\u96c6\u7684\u5217\u540d\u548c\u884c\u540d\u987a\u5e8f\u4e00\u81f4<\/p>\n

        if(!identical(rownames(logfcCat), rownames(p.valOrdered))) p.valOrdered <- p.valOrdered[rownames(logfcCat),]<\/p>\n

        if(!identical(colnames(logfcCat), colnames(p.valOrdered))) p.valOrdered <- p.valOrdered[colnames(logfcCat)]<\/p>\n

        ## \u628aP> 0.05\u7684\u6570\u636e\u6807\u8bb0\u4e3a P > 0.05<\/p>\n

        logfcCat[p.valOrdered >= 0.05] <- “P >= 0.05”<\/p>\n

        ## \u6bcf\u4e2a\u5206\u7c7b\u5b9a\u4e49\u4e00\u4e2a\u989c\u8272<\/p>\n

        col_cat <- c(“> 2” = “#A80C3A”, “1 – 2” = “#ED5E57”, “-1 – 1” = “#DDD3D2”,<\/p>\n

        “-2 – -1” = “#6B9AB7”, “< -2” = “#2F5B89”, “P >= 0.05” = “white”)<\/p>\n

        cell_fun <- function(logfc, dataP, logfcCutoff = 1, PCutoff = 0.05,<\/p>\n

        darkcol = “black”, lightcol = “white”, digit = 2, fontsize = 6){<\/p>\n

        function(j, i, x, y, width, height, fill){<\/p>\n

        if(abs(logfc[i,j]) > logfcCutoff & dataP[i,j] < PCutoff){<\/p>\n

        grid.text(round(logfc, digit)[i, j], x, y,<\/p>\n

        gp = gpar(fontsize = fontsize, col = lightcol))<\/p>\n

        }else{<\/p>\n

        grid.text(round(logfc, digit)[i, j], x, y,<\/p>\n

        gp = gpar(fontsize = fontsize, col = darkcol))<\/p>\n

        }<\/p>\n

        }<\/p>\n

        }<\/p>\n

        ## \u5b9a\u4e49\u6ce8\u91ca\u4fe1\u606f<\/p>\n

        row_an <- HeatmapAnnotation(type = genetype$type, ##\u6ce8\u91ca\u4fe1\u606f\u7684\u5185\u5bb9<\/p>\n

        show_annotation_name = F, ## \u662f\u5426\u663e\u793a\u6ce8\u91ca\u7684\u6807\u9898<\/p>\n

        col = list(type = an_col), ## \u6ce8\u91ca\u4fe1\u606f\u7684\u989c\u8272<\/p>\n

        show_legend = T, ## \u662f\u5426\u663e\u793a\u6ce8\u91ca\u4fe1\u606f\u7684\u8bf4\u660e<\/p>\n

        annotation_legend_param = list(title = “MMP Subtype”), ## \u6ce8\u91ca\u4fe1\u606f\u56fe\u4f8b\u7684\u6807\u9898<\/p>\n

        which = “row”) #\u5bf9\u884c\u6216\u8005\u5217\u8fdb\u884c\u6ce8\u91ca<\/p>\n

        pdf(“rankHeatmap.pdf”, width = 8, height = 4)<\/p>\n

        Heatmap(matrix = logfcCat,<\/p>\n

        name = “logFC”, #\u4e3b\u8981\u56fe\u4f8b\u7684\u6807\u9898<\/p>\n

        rect_gp = gpar(col = “NA”, lwd = 1), #\u4e0d\u753b\u8fb9\u6846\uff0c\u6216\u8005\u7528col = “grey”\u753b\u7070\u8272\u8fb9\u6846<\/p>\n

        col = col_cat, #\u70ed\u56fe\u989c\u8272<\/p>\n

        row_names_side = “left”,<\/p>\n

        cell_fun = cell_fun(logfcOrdered, p.valOrdered),<\/p>\n

        row_names_gp = gpar(fontsize = 8), #\u57fa\u56e0\u540d\u5b57\u53f7<\/p>\n

        column_names_gp = gpar(fontsize = 8), #\u80bf\u7624\u7c7b\u578b\u5b57\u53f7<\/p>\n

        column_names_rot = 45, #\u80bf\u7624\u7c7b\u578b\u544845\u5ea6<\/p>\n

        left_annotation = row_an) #\u5de6\u4fa7\u57fa\u56e0\u5206\u7c7b\uff0c\u5982\u679c\u4e0d\u753b\uff0c\u5c31\u7b5b\u6389\u8fd9\u4e2a\u53c2\u6570<\/p>\n

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

        \"Dingtalk_20230129161403\"<\/p>\n

        \u6700\u7ec8\u5c0f\u679c\u7ed8\u5236\u51fa\u4e86\u5206\u7c7b\u53d8\u91cf\u70ed\u56fe\uff0c\u770b\u8d77\u6765\u6548\u679c\u4e0d\u9519\uff0c\u6709\u9700\u8981\u7684\u53ef\u4ee5\u501f\u9274\u5b66\u4e60\u5965\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

        \u4eca\u5929\u5c0f\u679c\u7ed8\u5236\u4e00\u4e0b\u5206\u7c7b\u53d8\u91cf\u53d8\u91cf\u70ed\u56fe\uff0c\u7ed8\u5236\u8be5\u56fe\u9700\u8981\u4e09\u4e2a\u8f93\u5165\u6587\u4ef6\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a \u5b89\u88c5\u6240\u9700\u8981\u7684R\u5305 BiocManage […]<\/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\/28854"}],"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=28854"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/28854\/revisions"}],"predecessor-version":[{"id":28859,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/28854\/revisions\/28859"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=28854"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=28854"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=28854"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}