## ----load-packages, warning=FALSE, message=FALSE, echo=FALSE------------------ knitr::opts_chunk$set(cache =FALSE, autodep = TRUE, warning=FALSE, message=FALSE, echo= TRUE, eval = TRUE, tidy = TRUE，图.width = 9，图.height = 6, purl = TRUE，图.show = "hold"，缓存。lazy = FALSE) palStore = palette() #加载所有适合的，以避免每次重建vignette Load (system。文件(“extdata”、“zhangFits。RData”,包= "结合 ")) ## ---- 安装,eval = FALSE ---------------------------------------------------- # 库(BiocManager) # BiocManager::安装(“联合”,更新= FALSE) # #——installDevtools eval = FALSE -------------------------------------------- # 库(devtools) # install_github(“CenterForStatistics-UGent /联合 ") ## ---- loadcombipackage --------------------------------------------------------- suppressPackageStartupMessages(图书馆(联合))猫(“联合包版本”,as.character (packageVersion(“联合”)),“\ n ") ## ---- loadData ----------------------------------------------------------------- 数据(张)# #——unconstr ----------------------------------------------------------------- microMetaboInt =结合(列表(= zhangMicrobio“微生物”,“代谢组学”= zhangMetabo),分布= c(“准”、“高斯”),成分= c(真、假),logTransformGaussian = FALSE) # #——表演 --------------------------------------------------------------------- microMetaboInt # #——simplePlot --------------------------------------------------------------- 情节(microMetaboInt) # #——colourPlot --------------------------------------------------------------- 情节(microMetaboInt samDf = zhangMetavars samCol = " ABX ") ## ---- cloudPlot ---------------------------------------------------------------- 情节(microMetaboInt samDf = zhangMetavars,samCol = " ABX ", featurePlot = "点 ") ## ---- denPlot ------------------------------------------------------------------ 情节(microMetaboInt samDf = zhangMetavars samCol =“ABX featurePlot = "密度 ") ## ---- 预测 -------------------------------------------------------------- # 首先定义情节,并返回坐标mmPlot =情节(microMetaboInt, samDf = zhangMetavars samCol =“ABX returnCoords = TRUE, featNum = 10) #提供功能名称,和样品坐标,但允许通过addLink任意组合(mmPlot链接= cbind(“Staphylococcus_819c11”、“OTU929ffc”),观点= 1,样品= c (0, 1 )) ## ---- extractCoords ------------------------------------------------------------ 坐标= extractCoords (microMetaboInt昏暗= c(1、2 )) ## ---- 若干 ------------------------------------------------------------------- microMetaboIntConstr =结合(列表(= zhangMicrobio“微生物”,“代谢组学”= zhangMetabo),分布= c(“准”、“高斯”),成分= c(真、假),logTransformGaussian = FALSE,反是= zhangMetavars) # #——printConstr -------------------------------------------------------------- microMetaboIntConstr # #——colourPlotConstr --------------------------------------------------------- 情节(microMetaboIntConstr samDf = zhangMetavars,samCol = " ABX ") ## ---- convPlot ----------------------------------------------------------------- convPlot (microMetaboInt) # #——inflPlot ----------------------------------------------------------------- inflPlot (microMetaboInt样品= 1:20,plotType = "箱线图 ") ## ---- linFewVars eval = FALSE ------------------------------------------------- # # 线性只有两个变量# microMetaboIntConstr2Vars =结合(#列表(= zhangMicrobio“微生物”,“代谢组学”= zhangMetabo),#分布= c(“准”、“高斯”),成分= c(真、假),# logTransformGaussian = FALSE,反是= zhangMetavars [c(“性”、“ABX ")]) ## ---- plotFewVars -------------------------------------------------------------- 情节(microMetaboIntConstr2Vars samDf = zhangMetavars samCol = " ABX ") ## ---- 调整,eval = FALSE ------------------------------------------------------ # # 线性只有两个变量# microMetaboTweak =结合(#列表(= zhangMicrobio“微生物”,“代谢组学”= zhangMetabo), #分布= c(“准”、“高斯”),成分= c(真、假),# logTransformGaussian = FALSE, initPower = 1.5, minFraction = 0.25, prevCutOff = 0.8) # #——sessionInfo -------------------------------------------------------------- sessionInfo ()