{"id":67096,"date":"2026-11-14T19:46:14","date_gmt":"2026-11-14T11:46:14","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=67096"},"modified":"2026-11-14T20:45:38","modified_gmt":"2026-11-14T12:45:38","slug":"seurat-dotplot-dot-size-colour-detection-average","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/seurat-dotplot-dot-size-colour-detection-average\/","title":{"rendered":"Seurat \u6c14\u6ce1\u56fe\u600e\u4e48\u8bfb\uff1f\u7528\u56db\u4e2a\u7ec6\u80de\u770b\u61c2\u70b9\u7684\u5927\u5c0f\u548c\u989c\u8272"},"content":{"rendered":"
\n

\u7ed9\u4e24\u4e2a\u7ec6\u80de\u7fa4\u753b\u540c\u4e00\u4e2a\u6807\u8bb0\u57fa\u56e0\uff0c\u773c\u524d\u662f\u4e24\u4e2a\u51e0\u4e4e\u540c\u8272\u7684\u70b9\uff0c\u4e00\u5927\u4e00\u5c0f\u3002\u5199\u56fe\u6ce8\u65f6\u8be5\u7528\u201c\u8868\u8fbe\u66f4\u9ad8\u201d\uff0c\u8fd8\u662f\u201c\u8868\u8fbe\u7684\u7ec6\u80de\u66f4\u591a\u201d\uff1f\u5982\u679c\u4e24\u7fa4\u7eb3\u5165\u7684\u7ec6\u80de\u6570\u672c\u6765\u5c31\u4e0d\u540c\uff0c\u8fde\u201c\u66f4\u591a\u201d\u4e5f\u8981\u6362\u6210\u201c\u6bd4\u4f8b\u66f4\u9ad8\u201d\u3002\u5148\u628a\u6bcf\u4e2a\u70b9\u540e\u9762\u6709\u54ea\u4e9b\u7ec6\u80de\u3001\u5206\u6bcd\u53d6\u8c01\u5199\u51fa\u6765\uff0c\u7ec4\u4f1a\u4e0a\u7684\u4e89\u8bba\u5c31\u53ef\u4ee5\u76f4\u63a5\u7b97\u4e00\u904d\u3002<\/p>\n

\u4e0b\u9762\u56fa\u5b9a\u4e00\u4e2a\u5e38\u89c1\u7684\u4f5c\u56fe\u6761\u4ef6\u3002\u4f7f\u7528 Seurat \u7684 RNA assay\uff0c\u8868\u8fbe\u5c42\u5df2\u7ecf\u505a\u8fc7 LogNormalize\uff0c\u6309\u7ec6\u80de\u7fa4\u5206\u7ec4\u3002\u6574\u7406\u8fc7\u7684\u5bf9\u8c61\u53ef\u80fd\u9ed8\u8ba4\u6307\u5411\u522b\u7684 assay\uff0c\u5148\u5199\u660e\u6240\u7528\u6570\u636e\uff0c\u624d\u5bb9\u6613\u548c\u540c\u4e8b\u590d\u73b0\u540c\u4e00\u5f20\u56fe\u3002<\/p>\n

\u4ece\u56db\u4e2a\u7ec6\u80de\u7b97\u51fa\u4e00\u4e2a\u70b9<\/h2>\n

\u5047\u8bbe\u7532\u3001\u4e59\u4e24\u7fa4\u5404\u6709\u56db\u4e2a\u7ec6\u80de\u3002\u4e0b\u8868\u662f\u540c\u4e00\u57fa\u56e0\u5728\u6bcf\u4e2a\u7ec6\u80de\u91cc\u7684\u7ebf\u6027\u5f52\u4e00\u5316\u8868\u8fbe\u91cf\uff0c\u5373\u6309\u6bcf\u4e2a\u7ec6\u80de\u7684\u6d4b\u5e8f\u91cf\u5f52\u4e00\u5316\u540e\u3001\u53d6\u5bf9\u6570\u524d\u7684\u503c\u3002\u6570\u5b57\u4e13\u4e3a\u6f14\u793a\u9009\u53d6\uff0c\u62ff\u81ea\u5df1\u7684\u539f\u59cb UMI \u77e9\u9635\u65f6\u8981\u5148\u505a\u76f8\u5e94\u7684\u5f52\u4e00\u5316\u3002<\/p>\n

\n\n\n\n\n\n\n
\u7ec6\u80de\u7fa4<\/th>\n\u56db\u4e2a\u7ec6\u80de\u7684\u8868\u8fbe\u91cf<\/th>\n\u68c0\u51fa\u6bd4\u4f8b<\/th>\n\u5168\u7fa4\u5e73\u5747<\/th>\n<\/tr>\n<\/thead>\n
\u7532<\/td>\n4\u30014\u30010\u30010<\/td>\n2\/4 = 50%<\/td>\n(4 + 4) \/ 4 = 2<\/td>\n<\/tr>\n
\u4e59<\/td>\n8\u30010\u30010\u30010<\/td>\n1\/4 = 25%<\/td>\n8 \/ 4 = 2<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u7532\u7fa4\u6709\u4e00\u534a\u7ec6\u80de\u68c0\u51fa\uff0c\u4e59\u7fa4\u53ea\u6709\u56db\u5206\u4e4b\u4e00\uff0c\u6240\u4ee5\u7532\u7684\u70b9\u5e94\u5f53\u66f4\u5927\u3002\u4e24\u7fa4\u7684\u603b\u8868\u8fbe\u91cf\u90fd\u662f\u516b\uff0c\u9664\u4ee5\u5404\u81ea\u7684\u56db\u4e2a\u7ec6\u80de\uff0c\u5e73\u5747\u90fd\u662f\u4e8c\u3002\u82e5\u53ea\u5bf9\u68c0\u51fa\u7ec6\u80de\u53d6\u5e73\u5747\uff0c\u7532\u4f1a\u5f97\u5230\u56db\u3001\u4e59\u4f1a\u5f97\u5230\u516b\uff0c\u90a3\u662f\u53e6\u4e00\u4e2a\u95ee\u9898\u3002\u7528\u8fd9\u4e24\u4e2a\u6570\u5b57\u6765\u89e3\u91ca\u6c14\u6ce1\u989c\u8272\uff0c\u5c31\u628a\u5206\u6bcd\u6362\u6389\u4e86\u3002<\/p>\n

\u8fd9\u91cc\u8fd8\u6709\u4e00\u4e2a\u7ec6\u8282\u3002\u4e24\u7fa4\u7684\u5e73\u5747\u6570\u5b8c\u5168\u76f8\u540c\uff0c\u53ea\u753b\u8fd9\u4e24\u7fa4\u3001\u8fd9\u4e00\u4e2a\u57fa\u56e0\u65f6\uff0c\u9ed8\u8ba4\u7684\u6309\u57fa\u56e0\u6807\u51c6\u5316\u4f1a\u9047\u5230\u96f6\u65b9\u5dee\u3002\u628a scale = FALSE<\/code> \u7528\u4e8e\u8fd9\u4e2a\u5c0f\u4f8b\u5b50\uff0c\u4e24\u7fa4\u7684\u989c\u8272\u8f93\u5165\u90fd\u662f log1p(2)<\/code>\uff0c\u7ea6\u4e3a 1.099\u3002\u8981\u590d\u7b97\u68c0\u51fa\u7387\u4e0e\u5e73\u5747\u6570\uff0c\u53ef\u4ee5\u76f4\u63a5\u8fd0\u884c\u4e0b\u9762\u7684\u57fa\u7840 R \u4ee3\u7801\u3002<\/p>\n

x <- list(A = c(4, 4, 0, 0), B = c(8, 0, 0, 0))\r\nsapply(x, function(v) c(\r\n  pct = 100 * mean(v > 0),\r\n  avg = mean(v),\r\n  colour_unscaled = log1p(mean(v))\r\n))\r\n<\/code><\/pre>\n
\"\u6559\u5b66\u793a\u4f8b\u3002\u7532\u7ec4\u56db\u4e2a\u7ec6\u80de\u4e3a
\u56db\u4e2a\u7ec6\u80de\u7684\u6559\u5b66\u4f8b\u5b50\u3002\u5206\u6bcd\u59cb\u7ec8\u53d6\u5404\u7ec4\u5168\u90e8\u7ec6\u80de\uff0c\u53ef\u4ee5\u628a\u68c0\u51fa\u6bd4\u4f8b\u548c\u5e73\u5747\u8868\u8fbe\u5206\u522b\u7b97\u6e05\u3002<\/figcaption><\/figure>\n
\u9ed8\u8ba4\u989c\u8272\u4e3a\u4ec0\u4e48\u4f1a\u968f\u5206\u7ec4\u6539\u53d8<\/h2>\n
\u5728\u4e0a\u8ff0\u6761\u4ef6\u4e0b\uff0cSeurat \u5148\u628a\u6bcf\u4e2a\u7ec6\u80de\u7684\u5bf9\u6570\u5f52\u4e00\u5316\u8868\u8fbe\u8fd8\u539f\u5230\u7ebf\u6027\u5c3a\u5ea6\uff0c\u5bf9\u7ec4\u5185\u6240\u6709\u7ec6\u80de\u6c42\u5e73\u5747\uff0c\u518d\u5bf9\u5404\u7ec4\u5747\u503c\u53d6 log1p<\/code>\u3002\u9ed8\u8ba4\u5f00\u542f\u7684 scale = TRUE<\/code> \u8fd8\u4f1a\u5bf9\u540c\u4e00\u4e2a\u57fa\u56e0<\/strong>\u5728\u5404\u7ec4\u7684\u8fd9\u4e9b\u503c\u505a\u4e2d\u5fc3\u5316\u548c\u6807\u51c6\u5316\u3002\u6700\u540e\uff0c\u8272\u9636\u4e0a\u4e0b\u9650\u8fd8\u53ef\u80fd\u628a\u6781\u7aef\u503c\u622a\u5230\u540c\u4e00\u79cd\u989c\u8272\u3002\u8981\u77e5\u9053\u67d0\u4e2a\u6df1\u8272\u70b9\u4ee3\u8868\u4ec0\u4e48\uff0c\u5f97\u540c\u65f6\u77e5\u9053\u56fe\u91cc\u653e\u4e86\u54ea\u4e9b\u7fa4\u3002DotPlot \u53c2\u6570\u8bf4\u660e<\/a> \u00b7 Seurat v5.3.0 \u7684\u8ba1\u7b97\u5b9e\u73b0<\/a><\/p>\n
\u4e3e\u4e2a\u5e38\u89c1\u7684\u5b9e\u9645\u64cd\u4f5c\u3002\u4f60\u5148\u5728\u5168\u56fe\u8c31\u91cc\u753b\u4e00\u4e2a\u6dcb\u5df4\u7ec6\u80de\u6807\u8bb0\uff0c\u518d\u53ea\u9009\u51e0\u4e2a\u6dcb\u5df4\u4e9a\u7fa4\u91cd\u753b\u3002\u5373\u4fbf\u4fdd\u7559\u4e0b\u6765\u7684\u7ec6\u80de\u4e00\u4e2a\u4e5f\u6ca1\u53d8\uff0c\u7528\u6765\u8ba1\u7b97\u8be5\u57fa\u56e0\u76f8\u5bf9\u9ad8\u4f4e\u7684\u7ec4\u5df2\u7ecf\u6362\u4e86\uff0c\u540c\u4e00\u7fa4\u7684\u989c\u8272\u5c31\u53ef\u80fd\u6539\u53d8\u3002\u505a\u4e24\u9879\u76ee\u5bf9\u7167\u65f6\uff0c\u6700\u597d\u628a\u8981\u6bd4\u8f83\u7684\u7ec4\u653e\u8fdb\u540c\u4e00\u5bf9\u8c61\u3001\u4e00\u6b21\u4f5c\u56fe\uff0c\u5e76\u786e\u8ba4\u4e24\u8fb9\u4f7f\u7528\u540c\u6837\u7684\u8868\u8fbe\u5904\u7406\u3002\u82e5\u786e\u5b9e\u8981\u62c6\u6210\u4e24\u5f20\u56fe\uff0c\u9664\u5173\u95ed\u6309\u57fa\u56e0\u7f29\u653e\u5916\uff0c\u8fd8\u8981\u7ed9\u4e24\u5f20\u56fe\u8bbe\u7f6e\u76f8\u540c\u7684\u989c\u8272\u8303\u56f4\u3002\u5404\u81ea\u81ea\u52a8\u9009\u62e9\u7684\u8272\u9636\u4ecd\u4f1a\u8ba9\u540c\u4e00\u4e2a\u503c\u770b\u4e0a\u53bb\u4e0d\u4e00\u6837\u3002<\/p>\n
\u540c\u6837\u7684\u9053\u7406\u4e5f\u9002\u7528\u4e8e\u4e00\u5f20\u56fe\u91cc\u7684\u4e24\u4e2a\u57fa\u56e0\u3002\u7532\u57fa\u56e0\u7684\u4e00\u679a\u6df1\u8272\u70b9\u548c\u4e59\u57fa\u56e0\u7684\u4e00\u679a\u6d45\u8272\u70b9\uff0c\u5404\u81ea\u90fd\u6709\u4e00\u7ec4\u7528\u6765\u6807\u51c6\u5316\u7684\u5747\u503c\u3002\u82e5\u8981\u6bd4\u8f83\u4e24\u4e2a\u57fa\u56e0\u7684\u6570\u503c\uff0c\u5e94\u67e5\u770b\u539f\u59cb\u7edf\u8ba1\u8868\uff0c\u5e76\u4ea4\u4ee3\u8868\u8fbe\u5355\u4f4d\u4e0e\u5f52\u4e00\u5316\u65b9\u6cd5\u3002\u5149\u51ed\u989c\u8272\uff0c\u6700\u591a\u80fd\u63cf\u8ff0\u67d0\u4e2a\u6807\u8bb0\u5728\u6240\u753b\u5404\u7fa4\u4e2d\u7684\u76f8\u5bf9\u5206\u5e03\u3002LogNormalize \u7684\u5b9a\u4e49<\/a><\/p>\n
\u4ece\u81ea\u5df1\u7684\u56fe\u91cc\u53d6\u56de\u90a3\u4e24\u4e2a\u6570<\/h2>\n
\u5047\u5b9a\u4f60\u7684\u5bf9\u8c61\u53eb obj<\/code>\uff0c\u5143\u6570\u636e\u91cc\u6709\u5df2\u7ecf\u68c0\u67e5\u8fc7\u7684 celltype<\/code> \u5217\u3002\u4e0b\u9762\u4ee5\u4eba\u7c7b\u514d\u75ab\u7ec6\u80de\u5e38\u89c1\u7684\u4e24\u4e2a\u6807\u8bb0\u4e3a\u4f8b\u3002\u5176\u4ed6\u7269\u79cd\u6216\u4f7f\u7528 Ensembl ID \u7684\u5bf9\u8c61\uff0c\u8bf7\u628a\u57fa\u56e0\u540d\u6362\u6210\u8868\u8fbe\u77e9\u9635\u5b9e\u9645\u4f7f\u7528\u7684\u6807\u8bc6\u3002\u5148\u7528 table(obj$celltype)<\/code> \u770b\u770b\u6bcf\u4e2a\u70b9\u80cc\u540e\u6709\u591a\u5c11\u7ec6\u80de\uff0c\u518d\u753b\u56fe\u3001\u53d6\u6570\u3002<\/p>\n
library(Seurat)\r\ntable(obj$celltype)\r\np <- DotPlot(obj, features = c("CD3D", "MS4A1"),\r\n             assay = "RNA", group.by = "celltype",\r\n             scale = FALSE, dot.min = 0)\r\np\r\np$data[, c("id", "features.plot", "pct.exp", "avg.exp")]\r\n<\/code><\/pre>\n
\u5728\u8fd9\u4efd\u8f93\u51fa\u91cc\uff0cpct.exp<\/code> \u6309\u767e\u5206\u6570\u7ed9\u51fa\uff0c\u4f8b\u5982 25 \u5c31\u662f\u767e\u5206\u4e4b\u4e8c\u5341\u4e94\u3002avg.exp<\/code> \u662f\u7ebf\u6027\u5c3a\u5ea6\u7684\u7ec4\u5185\u5747\u503c\uff0c\u5305\u542b\u96f6\u503c\u3002\u56de\u5230\u56fe\u4e0a\u65f6\uff0c\u70b9\u7684\u5927\u5c0f\u8bf7\u5bf9\u5e94\u56fe\u4f8b\u8bfb\u6570\u3002\u9ed8\u8ba4\u8bbe\u7f6e\u8fd8\u6d89\u53ca\u6309\u534a\u5f84\u6620\u5c04\uff0c\u8089\u773c\u4f30\u8ba1\u5706\u9762\u79ef\u5f88\u5bb9\u6613\u9ad8\u4f30\u6bd4\u4f8b\u5dee\u5f02\u3002\u82e5\u522b\u4eba\u53d1\u6765\u7684\u56fe\u4e0a\u67d0\u5904\u5b8c\u5168\u7559\u767d\uff0c\u5148\u95ee\u662f\u5426\u8bbe\u7f6e\u4e86 dot.min<\/code>\u3002\u4f4e\u4e8e\u663e\u793a\u9608\u503c\u7684\u70b9\u4f1a\u88ab\u9690\u85cf\uff0c\u5373\u4f7f\u539f\u672c\u786e\u5b9e\u6709\u5c11\u91cf\u7ec6\u80de\u68c0\u51fa\u3002<\/p>\n
\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u6253\u5f00\u771f\u5b9e\u56fe\u5bf9\u8c61\uff0c\u68c0\u67e5\u7ed8\u56fe\u7528\u7684\u4e09\u5217\u6570<\/h2>\n
\u6211\u4eec\u7528 R 4.3.3 \u5b9e\u9645\u5b89\u88c5\u5e76\u8fd0\u884c Seurat 5.0.1\u3002\u5148\u5efa\u516b\u5217\u8ba1\u6570\uff0c\u6bcf\u5217\u8865\u8db3\u81f3\u4e00\u4e07\u4e2a\u5206\u5b50\uff0c\u8ba9 LogNormalize \u7684\u7ebf\u6027\u5f52\u4e00\u5316\u503c\u4e0e\u4e0a\u9762\u7684\u624b\u7b97\u5b8c\u5168\u4e00\u81f4\u3002\u7528\u540c\u4e00\u4e2a DotPlot \u5bf9\u8c61\u53d6\u6570\uff0c\u7532\u3001\u4e59\u7684\u68c0\u51fa\u6bd4\u4f8b\u4f9d\u6b21\u662f 50 \u548c 25\uff0c\u7ebf\u6027\u5747\u503c\u90fd\u662f 2\uff0c\u5173\u95ed\u6309\u57fa\u56e0\u7f29\u653e\u540e\u7684\u989c\u8272\u503c\u4e5f\u540c\u4e3a 1.098612\u3002\u8bfb\u56fe\u65f6\u5982\u679c\u53ea\u4fdd\u5b58\u767e\u5206\u6bd4\u548c\u989c\u8272\u622a\u56fe\uff0c\u540e\u6765\u5c06\u770b\u4e0d\u51fa\u8fd9\u4e2a\u76f8\u540c\u7684\u989c\u8272\u7a76\u7adf\u5bf9\u5e94\u54ea\u4e2a\u7ebf\u6027\u5747\u503c\u3002\u628a\u56fe\u5bf9\u8c61\u91cc\u7684\u4e09\u5217\u8fde\u540c\u5206\u7ec4\u540d\u4e00\u5e76\u5bfc\u51fa\uff0c\u5c31\u80fd\u9010\u9879\u590d\u6838\u3002<\/p>\n
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