"use strict"; const {jsx: _jsx, jsxs: _jsxs} = arguments[0]; const {useMDXComponents: _provideComponents} = arguments[0]; function _createMdxContent(props) { const _components = { code: "code", pre: "pre", span: "span", ..._provideComponents(), ...props.components }; return _jsx(_components.pre, { className: "language-r", children: _jsxs(_components.code, { className: "language-R code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#####################################################################################################################################################################################" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "########################################################++++++++++++------ScRNA-seq------++++++++++++################################################################################" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#####################################################################################################################################################################################" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "################################### 01.install R packages ###################################" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["install.packages", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"Seurat\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["install.packages", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"outliers\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { 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children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["BiocManager", _jsx(_components.span, { className: "token operator", children: "::" }), "install", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"GSEABase\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["BiocManager", _jsx(_components.span, { className: "token operator", children: "::" }), "install", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"limma\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["install.packages", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"devtools\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["library", _jsx(_components.span, { className: "token punctuation", children: "(" }), "devtools", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["install.packages", _jsx(_components.span, { className: "token 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className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "# 再不行用这个，SingleR安装极为麻烦，对网络要求极高" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# check with library" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "################################### 02.下机数据质控 ###################################" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step1 引用R包" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["library", _jsx(_components.span, { className: "token punctuation", children: "(" }), "limma", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["library", _jsx(_components.span, { className: "token punctuation", children: "(" }), "Seurat", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["library", _jsx(_components.span, { className: "token punctuation", children: "(" }), "dplyr", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["library", _jsx(_components.span, { className: "token punctuation", children: "(" }), "magrittr", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["library", _jsx(_components.span, { className: "token punctuation", children: "(" }), "patchwork", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step2 设置工作路径" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["setwd", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"E:\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#设置工作路径" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step3-1 取均值处理（非常重要：只有我们的数据是GeneMatrix,即行为细胞样，列为基因的矩阵时才需要这一步。）" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["rt", _jsx(_components.span, { className: "token operator", children: "=" }), "read.table", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"文件名\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "sep", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"\\t\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "header", _jsx(_components.span, { className: "token operator", children: "=" }), "T", _jsx(_components.span, { className: "token punctuation", children: "," }), "check.names", _jsx(_components.span, { className: "token operator", children: "=" }), "F", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#读取文件，并对重复基因取均值 #按\\t分格 #有表头 #对它的名字不检查" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["rt", _jsx(_components.span, { className: "token operator", children: "=" }), "as.matrix", _jsx(_components.span, { className: "token punctuation", children: "(" }), "rt", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#将数据转换为矩阵" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["rownames", _jsx(_components.span, { className: "token punctuation", children: "(" }), "rt", _jsx(_components.span, { className: "token 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}), "rt", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["dimnames", _jsx(_components.span, { className: "token operator", children: "=" }), "list", _jsx(_components.span, { className: "token punctuation", children: "(" }), "rownames", _jsx(_components.span, { className: "token punctuation", children: "(" }), "exp", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "colnames", _jsx(_components.span, { className: "token punctuation", children: "(" }), "exp", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["data", _jsx(_components.span, { className: "token operator", children: "=" }), "matrix", _jsx(_components.span, { className: "token punctuation", children: "(" }), "as.numeric", _jsx(_components.span, { className: "token punctuation", children: "(" }), "as.matrix", _jsx(_components.span, { className: "token punctuation", children: "(" }), "exp", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "nrow", _jsx(_components.span, { className: "token operator", children: "=" }), "nrow", _jsx(_components.span, { className: "token punctuation", children: "(" }), "exp", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "dimnames", _jsx(_components.span, { className: "token operator", children: "=" }), "dimnames", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["data", _jsx(_components.span, { className: "token operator", children: "=" }), "avereps", _jsx(_components.span, { className: "token punctuation", children: "(" }), "data", _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "#如果一个基因存在于多行，就会对基因取均值" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step3-2 Read10X（如果我们的数据不是GeneMatrix，而是\"matrix.mtx.gz\"+\"features.tsv.gz\"+\"barcodes.tsv.gz\"时需要这一步）" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#（注：barcodes.tsv.gz ---包含细胞的id；features.tsv.gz ---和基因相关的注释；matrix.mtx.gz---某个细胞里基因的一个值）" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs.data ", _jsx(_components.span, { className: "token operator", children: "<-" }), " Read10X", _jsx(_components.span, { className: "token punctuation", children: "(" }), "data.dir ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"E:\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["dir", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"E:\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#注：rt=read.table和Read10X是针对不同测序平台的输入代码" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "#step4 将矩阵转换为Seurat对象，并对数据进行过滤" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " CreateSeuratObject", _jsx(_components.span, { className: "token punctuation", children: "(" }), "counts ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs.data", _jsx(_components.span, { className: "token punctuation", children: "," }), " project ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"LD_MuSCs\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " min.cells ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "3" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " min.features ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "500" }), _jsx(_components.span, { className: "token punctuation", children: "," }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#如果数据类型是GeneMAtrix格式，还要加上 names.delim = \"_\"," }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#创建一个对象#数据即为读取的数据 #所创建对象的名字 #最小的细胞数目 #细胞测得基因数小于500，则删掉 #样品名分隔符，按下划线分割" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "LD_MuSCs\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "#step5 PercentageFeatureSet函数计算线粒体基因的百分比" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token string", children: "\"percent.mt\"" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token operator", children: "<-" }), " PercentageFeatureSet", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " pattern ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"^MT-\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#The [[ operator can add columns to object metadata. This is a great place to stash QC stats" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pdf", _jsx(_components.span, { className: "token punctuation", children: "(" }), "file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"02.step5.featureViolin.pdf\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "width", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "10" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "height", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "6" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#保存基因特征小提琴图" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["VlnPlot", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " features ", _jsx(_components.span, { className: "token operator", children: "=" }), " c", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"nFeature_RNA\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token string", children: "\"nCount_RNA\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token string", children: "\"percent.mt\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ncol ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "3" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["dev.off", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#关闭" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "#step6 对数据进行过滤" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " subset", _jsx(_components.span, { className: "token punctuation", children: "(" }), "LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " subset ", _jsx(_components.span, { className: "token operator", children: "=" }), " nFeature_RNA ", _jsx(_components.span, { className: "token operator", children: ">" }), " ", _jsx(_components.span, { className: "token number", children: "800" }), " ", _jsx(_components.span, { className: "token operator", children: "&" }), " nFeature_RNA ", _jsx(_components.span, { className: "token operator", children: "<" }), " ", _jsx(_components.span, { className: "token number", children: "4000" }), " ", _jsx(_components.span, { className: "token operator", children: "&" }), " percent.mt ", _jsx(_components.span, { className: "token operator", children: "<" }), " ", _jsx(_components.span, { className: "token number", children: "0.02" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#保留基因数目大于X的细胞 #线粒体基因百分率大于X%的细胞删掉" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# step5和step6出现问题就敲0" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "LD_MuSCs\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "#step7 测序深度的相关性绘图" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pdf", _jsx(_components.span, { className: "token punctuation", children: "(" }), "file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"02.step7.featureCor.pdf\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "width", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "10" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "height", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "6" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#保存基因特征相关性图" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["plot1 ", _jsx(_components.span, { className: "token operator", children: "<-" }), " FeatureScatter", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " feature1 ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"nCount_RNA\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " feature2 ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"percent.mt\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "pt.size", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["plot2 ", _jsx(_components.span, { className: "token operator", children: "<-" }), " FeatureScatter", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " feature1 ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"nCount_RNA\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " feature2 ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"nFeature_RNA\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "pt.size", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["CombinePlots", _jsx(_components.span, { className: "token punctuation", children: "(" }), "plots ", _jsx(_components.span, { className: "token operator", children: "=" }), " list", _jsx(_components.span, { className: "token punctuation", children: "(" }), "plot1", _jsx(_components.span, { className: "token punctuation", children: "," }), " plot2", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["dev.off", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#关闭" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "#step8 对数据进行标准化" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " NormalizeData", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " normalization.method ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"LogNormalize\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " scale.factor ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "10000" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#对对象进行标准化 #标准化的方法为取log #把测序深度矫正为100000（测序深度：测序得到的碱基总量（bp）与基因组大小（Genome）的比值，它是评价测序量的指标之一） " }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "#step9 提取那些在细胞间变异系数较大的基因" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " FindVariableFeatures", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " selection.method ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"vst\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " nfeatures ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "2000" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#找出对变异较大的基因 #找前1000个" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "#step10 输出特征方差图" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["top10 ", _jsx(_components.span, { className: "token operator", children: "<-" }), " head", _jsx(_components.span, { className: "token punctuation", children: "(" }), "x ", _jsx(_components.span, { className: "token operator", children: "=" }), " VariableFeatures", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token number", children: "10" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#把前十个变异最大的基因名字标上" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pdf", _jsx(_components.span, { className: "token punctuation", children: "(" }), "file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"02.step10.featureVar.pdf\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "width", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "10" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "height", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "6" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#保存基因特征方差图" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["plot1 ", _jsx(_components.span, { className: "token operator", children: "<-" }), " VariableFeaturePlot", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#把基因在样品间波动的图形绘制出来" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["plot2 ", _jsx(_components.span, { className: "token operator", children: "<-" }), " LabelPoints", _jsx(_components.span, { className: "token punctuation", children: "(" }), "plot ", _jsx(_components.span, { className: "token operator", children: "=" }), " plot1", _jsx(_components.span, { className: "token punctuation", children: "," }), " points ", _jsx(_components.span, { className: "token operator", children: "=" }), " top10", _jsx(_components.span, { className: "token punctuation", children: "," }), " repel ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token boolean", children: "TRUE" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#除了把基因在样品间的波动绘制出来，还要进行一个标注" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["CombinePlots", _jsx(_components.span, { className: "token punctuation", children: "(" }), "plots ", _jsx(_components.span, { className: "token operator", children: "=" }), " list", _jsx(_components.span, { className: "token punctuation", children: "(" }), "plot1", _jsx(_components.span, { className: "token punctuation", children: "," }), " plot2", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#把两个图形放在一起" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["dev.off", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "################################### 03.01 数据降维-PCA主成分分析 ###################################" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step1 引用R包" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["library", _jsx(_components.span, { className: "token punctuation", children: "(" }), "limma", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["library", _jsx(_components.span, { className: "token punctuation", children: "(" }), "Seurat", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["library", _jsx(_components.span, { className: "token punctuation", children: "(" }), "dplyr", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["library", _jsx(_components.span, { className: "token punctuation", children: "(" }), "magrittr", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step2 设置工作目录" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["setwd", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#如果之前做了，就不用做了" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step3 PCA分析" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), 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_jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " ScaleData", _jsx(_components.span, { className: "token punctuation", children: "(" }), "LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " vars.to.regress ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"percent.mt\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#PCA降维之前的标准预处理步骤" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " RunPCA", _jsx(_components.span, { className: "token punctuation", children: "(" }), "LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " features ", _jsx(_components.span, { className: "token operator", children: "=" }), " VariableFeatures", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#确认目标 #确认维度（即基因的数量） #把前面选出来的波动较大的基因作主成分分析" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step4 绘制每个PCA成分的相关基因图" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pdf", _jsx(_components.span, { className: "token punctuation", children: "(" }), "file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"03.01.step4.pcaGene.pdf\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "width", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "10" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "height", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "8" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["VizDimLoadings", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " dims ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token operator", children: ":" }), _jsx(_components.span, { className: "token number", children: "4" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " reduction ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"pca\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "nfeatures ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "20" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#确认目标 #绘制前4个主成分图 #降维方法 #呈现前多少个基因" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["dev.off", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step5 绘制主成分分析图形" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pdf", _jsx(_components.span, { className: "token punctuation", children: "(" }), "file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"03.01.step5.PCA.pdf\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "width", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "6.5" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "height", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "6" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: 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className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step6 绘制主成分分析热图" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pdf", _jsx(_components.span, { className: "token punctuation", children: "(" }), "file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"03.01.step6.pcaHeatmap.pdf\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "width", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "10" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "height", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "8" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["DimHeatmap", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " dims ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token operator", children: ":" }), _jsx(_components.span, { className: "token number", children: "15" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " cells ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "500" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " balanced ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token boolean", children: "TRUE" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " nfeatures ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "30" }), _jsx(_components.span, { className: "token punctuation", children: "," }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#画前4个PC #包含500个细胞 #每一行放2个热图 #" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["dev.off", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step7 绘制每个PC的p值分布和均匀分布" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " JackStraw", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " num.replicate ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "100" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#数据模拟100次" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " ScoreJackStraw", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " dims ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token operator", children: ":" }), _jsx(_components.span, { className: "token number", children: "20" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pdf", _jsx(_components.span, { className: "token punctuation", children: "(" }), "file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"03.01.step7.pcaJackStraw.pdf\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "width", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "8" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "height", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "6" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["JackStrawPlot", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " dims ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token operator", children: ":" }), _jsx(_components.span, { className: "token number", children: "20" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["dev.off", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step8 绘制肘图" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pdf", _jsx(_components.span, { className: "token punctuation", children: "(" }), "file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"03.01.step8.ElbowPlot.pdf\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "width", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "8" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "height", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "6" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["ElbowPlot", _jsx(_components.span, { className: "token punctuation", children: "(" }), "LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["dev.off", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "################################### 03.02 数据降维-TSNE/UMAP聚类分析和marker基因 ###################################" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "#???? Look at cluster IDs of the first 5 cells" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["head", _jsx(_components.span, { className: "token punctuation", children: "(" }), "Idents", _jsx(_components.span, { className: "token punctuation", children: "(" }), "LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token number", children: "5" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step1-1 TSNE聚类" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pcSelect", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "15" }), " ", _jsx(_components.span, { className: "token comment", children: "#选择前20个主成分分析" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " FindNeighbors", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " dims ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token operator", children: ":" }), "pcSelect", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#80 #计算邻接距离" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " FindClusters", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " resolution ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "0.5" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#81 #对细胞分组,优化标准模块化" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " RunTSNE", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " dims ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token operator", children: ":" }), "pcSelect", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#83 #TSNE聚类" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pdf", _jsx(_components.span, { className: "token punctuation", children: "(" }), "file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"03.02.step1.TSNE.pdf\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "width", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "6.5" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "height", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "6" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["TSNEPlot", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " pt.size ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " label ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token boolean", children: "TRUE" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#TSNE可视化 pt.size = 2 #点的大小" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["dev.off", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step1-2 UMAP聚类" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pcSelect", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "15" }), " \n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " FindNeighbors", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " dims ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token operator", children: ":" }), "pcSelect", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#80 #计算邻接距离" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " FindClusters", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " resolution ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "0.5" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#81 #对细胞分组,优化标准模块化 " }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["LD_MuSCs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " RunUMAP", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " dims ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token operator", children: ":" }), "pcSelect", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["DimPlot", _jsx(_components.span, { className: "token punctuation", children: "(" }), "LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " reduction ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"umap\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " label ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token boolean", children: "TRUE" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#You can save the object at this point so that it can easily be loaded back in without having to rerun the computationally intensive steps performed above, or easily shared with collaborators." }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["saveRDS", _jsx(_components.span, { className: "token punctuation", children: "(" }), "pbmc", _jsx(_components.span, { className: "token punctuation", children: "," }), " file ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"../LD_MuSCs.rds\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step2" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["write.table", _jsx(_components.span, { className: "token punctuation", children: "(" }), "LD_MuSCs", _jsx(_components.span, { className: "token operator", children: "$" }), "seurat_clusters", 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_jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step3 寻找差异表达的特征/找到所有cluster的marker" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["logFCfilter", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "0" }), " ", _jsx(_components.span, { className: "token comment", children: "#改为0.25后可大大提高速度" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["adjPvalFilter", _jsx(_components.span, { className: "token operator", children: "=" }), 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"token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token comment", children: "#Only return positive markers (FALSE by default)" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" min.pct ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token comment", children: "#定义最小的pct值" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" logfc.threshold ", _jsx(_components.span, { className: "token operator", children: "=" }), " logFCfilter", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#过滤" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["sig.markers ", _jsx(_components.span, { className: "token operator", children: "<-" }), " LD_MuSCs.markers", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "abs", _jsx(_components.span, { className: "token punctuation", children: "(" }), "as.numeric", _jsx(_components.span, { className: "token punctuation", children: "(" }), "as.vector", _jsx(_components.span, { className: "token punctuation", children: "(" }), "LD_MuSCs.markers", _jsx(_components.span, { className: "token operator", children: "$" }), "avg_logFC", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token operator", children: ">" }), "logFCfilter ", _jsx(_components.span, { className: "token operator", children: "&" }), " as.numeric", _jsx(_components.span, { className: "token punctuation", children: "(" }), "as.vector", _jsx(_components.span, { className: "token punctuation", children: "(" }), "LD_MuSCs.markers", _jsx(_components.span, { className: "token operator", children: "$" }), "p_val_adj", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token operator", children: "<" }), "adjPvalFilter", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "," }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token comment", children: "#再过滤" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["write.table", _jsx(_components.span, { className: "token punctuation", children: "(" }), "sig.markers", _jsx(_components.span, { className: "token punctuation", children: "," }), " file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"03.step3.markers.xls\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " sep", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"\\t\"" 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"code-line", children: ["cluster1.markers ", _jsx(_components.span, { className: "token operator", children: "<-" }), " FindMarkers", _jsx(_components.span, { className: "token punctuation", children: "(" }), "LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " ident.", _jsx(_components.span, { className: "token number", children: "1" }), " ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "2" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " min.pct ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["head", _jsx(_components.span, { className: "token punctuation", children: "(" }), "cluster1.markers", _jsx(_components.span, { className: "token punctuation", children: "," }), " n ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "5" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "###step3-1 find all markers distinguishing cluster 5 from clusters 0 and 3" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["cluster5.markers ", _jsx(_components.span, { className: "token operator", children: "<-" }), " FindMarkers", _jsx(_components.span, { className: "token punctuation", children: "(" }), "LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " ident.", _jsx(_components.span, { className: "token number", children: "1" }), " ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "5" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ident.", _jsx(_components.span, { className: "token number", children: "2" }), " ", _jsx(_components.span, { className: "token operator", children: "=" }), " c", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token number", children: "3" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " min.pct ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "0.25" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["head", _jsx(_components.span, { className: "token punctuation", children: "(" }), "cluster5.markers", _jsx(_components.span, { className: "token punctuation", children: "," }), " n ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "5" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step4 绘制热图" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["top10 ", _jsx(_components.span, { className: "token operator", children: "<-" }), " LD_MuSCs.markers ", _jsx(_components.span, { className: "token percent-operator operator", children: "%>%" }), " group_by", _jsx(_components.span, { className: "token punctuation", children: "(" }), "cluster", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token percent-operator operator", children: "%>%" }), " top_n", _jsx(_components.span, { className: "token punctuation", children: "(" }), "n ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "10" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " wt ", _jsx(_components.span, { className: "token operator", children: "=" }), " avg_logFC", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#绘制marker在各个cluster的热图" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pdf", _jsx(_components.span, { className: "token punctuation", children: "(" }), "file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"03.step4.tsneHeatmap-top10.pdf\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "width", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "12" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "height", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "9" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["DoHeatmap", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " features ", _jsx(_components.span, { className: "token operator", children: "=" }), " top10", _jsx(_components.span, { className: "token operator", children: "$" }), "gene", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token operator", children: "+" }), " NoLegend", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["dev.off", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step5 绘制marker的小提琴图" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pdf", _jsx(_components.span, { className: "token punctuation", children: "(" }), "file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"03.step5.markerViolin.pdf\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "width", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "10" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "height", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "6" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["VlnPlot", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: "," }), " features ", _jsx(_components.span, { className: "token operator", children: "=" }), " c", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"IGLL5\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token string", children: "\"MBOAT1\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#选自己要研究的marker就好" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["dev.off", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step6 绘制marker在各个cluster的散点图" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pdf", _jsx(_components.span, { className: "token punctuation", children: "(" }), "file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"03.step6.markerScatter.pdf\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " width", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "6.5" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " height", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "6" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["FeaturePlot", _jsx(_components.span, { className: "token punctuation", children: "(" }), "object ", _jsx(_components.span, { className: "token operator", children: "=" }), " LD_MuSCs", _jsx(_components.span, { className: "token punctuation", children: 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["pdf", _jsx(_components.span, { className: "token punctuation", children: "(" }), "file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"03.step7.markerBubble.pdf\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "width", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "12" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "height", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "6" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["cluster10Marker", _jsx(_components.span, { className: "token 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[_jsx(_components.span, { className: "token comment", children: "#step8 Single cell ridge plot" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#details：https://github.com/satijalab/seurat/blob/master/R/visualization.R" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: 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_jsx(_components.span, { className: "token operator", children: "@" }), "meta.data", _jsx(_components.span, { className: "token operator", children: "$" }), "seurat_clusters\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["ann", _jsx(_components.span, { className: "token operator", children: "=" }), "pbmc", _jsx(_components.span, { className: "token operator", children: "@" }), "meta.data", _jsx(_components.span, { className: "token operator", children: "$" }), "orig.ident ", _jsx(_components.span, { className: "token comment", children: "#注释文件" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#step3 注释细胞" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["singler ", _jsx(_components.span, { className: "token operator", children: "=" }), " CreateSinglerObject", _jsx(_components.span, { className: "token punctuation", children: "(" }), "counts", _jsx(_components.span, { className: "token punctuation", children: "," }), " annot ", _jsx(_components.span, { className: "token operator", children: "=" }), " ann", _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token string", children: "\"pbmc\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " min.genes ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token comment", children: "#创建注释包的对象 #基因的表达 #细胞来源于哪个样品 ##已经过滤不需要过滤" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" species ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"Human\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " citation ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ref.list ", _jsx(_components.span, { className: "token operator", children: "=" }), " list", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " normalize.gene.length ", _jsx(_components.span, { className: "token operator", children: "=" }), " F", _jsx(_components.span, { className: "token punctuation", children: "," }), " variable.genes ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"de\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" fine.tune ", _jsx(_components.span, { className: "token operator", children: "=" }), " F", _jsx(_components.span, { className: "token punctuation", children: "," }), " do.signatures ", _jsx(_components.span, { className: "token operator", children: "=" }), " T", _jsx(_components.span, { className: "token punctuation", children: "," }), " clusters ", _jsx(_components.span, { className: "token operator", children: "=" }), " clusters", _jsx(_components.span, { className: "token punctuation", children: "," }), " do.main.types ", _jsx(_components.span, { className: "token operator", children: "=" }), " T", _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token comment", children: "#是否精细计算 " }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" reduce.file.size ", _jsx(_components.span, { className: "token operator", children: "=" }), " T", _jsx(_components.span, { className: "token punctuation", children: "," }), " numCores ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#选择Cpu核心的个数" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["singler", _jsx(_components.span, { className: "token operator", children: "$" }), "seurat ", _jsx(_components.span, { className: "token operator", children: "=" }), " pbmc\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["singler", _jsx(_components.span, { className: "token operator", children: "$" }), "meta.data", _jsx(_components.span, { className: "token operator", children: "$" }), "xy ", _jsx(_components.span, { className: "token operator", children: "=" }), " pbmc", _jsx(_components.span, { className: "token operator", children: "@" }), "reductions", _jsx(_components.span, { className: "token operator", children: "$" }), "tsne", _jsx(_components.span, { className: "token operator", children: "@" }), "cell.embeddings\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["clusterAnn", _jsx(_components.span, { className: "token operator", children: "=" }), "singler", _jsx(_components.span, { className: "token operator", children: "$" }), "singler", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token number", children: "2" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token operator", children: "$" }), "SingleR.clusters.main", _jsx(_components.span, { className: "token operator", children: "$" }), "labels ", _jsx(_components.span, { className: "token comment", children: "#保存结果文件" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["write.table", _jsx(_components.span, { className: "token punctuation", children: "(" }), "clusterAnn", _jsx(_components.span, { className: "token punctuation", children: "," }), "file", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"07.clusterAnn.txt\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "quote", _jsx(_components.span, { className: "token operator", children: "=" }), "F", _jsx(_components.span, { className: "token punctuation", children: "," }), "sep", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"\\t\"" }), _jsx(_components.span, { className: "token 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"sep", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"\\t\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "col.names", _jsx(_components.span, { className: "token operator", children: "=" }), "F", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#输出文件" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "################################### 04.02 注释细胞类型（手注）###################################" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", 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_jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "################################### 05 拟时分析（部分） ###################################" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#准备monocle分析需要的文件" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["monocle.matrix", _jsx(_components.span, { className: "token operator", children: "=" }), "as.matrix", _jsx(_components.span, { className: "token punctuation", children: "(" }), "pbmc", _jsx(_components.span, { 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...props.components }; return MDXLayout ? _jsx(MDXLayout, { ...props, children: _jsx(_createMdxContent, { ...props }) }) : _createMdxContent(props); } return { default: MDXContent };