## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----echo = FALSE, message=FALSE,warning=FALSE, eval=FALSE, echo=TRUE--------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("scTHI") ## ----warning=FALSE------------------------------------------------------------ library(scTHI) library(scTHI.data) set.seed(1234) data("H3K27") data("H3K27.meta") ## ----------------------------------------------------------------------------- table(H3K27.meta$Type) ## ----------------------------------------------------------------------------- Malignant <- rownames(H3K27.meta)[H3K27.meta$Type == "Malignant"][1:100] Immune <- rownames(H3K27.meta)[H3K27.meta$Type == "Immune cell"] ## ---- warning=FALSE----------------------------------------------------------- H3K27.result <- scTHI_score( expMat = H3K27, cellCusterA = Malignant, cellCusterB = Immune, cellCusterAName = "Malignant", cellCusterBName = "Immune", topRank = 10, PValue = TRUE, pvalueCutoff = 0.05, nPermu = 10, ncore = 1 ) ## ----------------------------------------------------------------------------- head(H3K27.result$result) ## ----------------------------------------------------------------------------- scTHI_plotResult(scTHIresult = H3K27.result, cexNames = 0.7, plotType = "score") ## ----------------------------------------------------------------------------- scTHI_plotResult(scTHIresult = H3K27.result, cexNames = 0.7, plotType = "pair") ## ----------------------------------------------------------------------------- H3K27.result <- scTHI_runTsne(scTHIresult = H3K27.result) ## ----------------------------------------------------------------------------- scTHI_plotCluster(scTHIresult = H3K27.result, cexPoint = 0.8, legendPos = "bottomleft") ## ----------------------------------------------------------------------------- scTHI_plotPairs( scTHIresult = H3K27.result, cexPoint = 0.8, interactionToplot = "THY1_ITGAX:ITGB2" ) ## ----------------------------------------------------------------------------- Tme.cells <- rownames(H3K27.meta)[which(H3K27.meta$Type != "Malignant")] H3K27.tme <- H3K27[, Tme.cells] ## ---- message=FALSE----------------------------------------------------------- Class <- TME_classification(expMat = H3K27.tme, minLenGeneSet = 10) ## ----------------------------------------------------------------------------- table(Class$Class[Tme.cells], H3K27.meta[Tme.cells, "Type"]) ## ----------------------------------------------------------------------------- TME_plot(tsneData = H3K27.result$tsneData, Class, cexPoint = 0.8) ## ----------------------------------------------------------------------------- sessionInfo()