## ----style, echo=FALSE, results='hide', message=FALSE------------------------- library(BiocStyle) library(knitr) opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE) knitr::opts_chunk$set(echo = TRUE) ## ----eval = FALSE------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("DepecheR") ## ----------------------------------------------------------------------------- library(DepecheR) data("testData") data("testDataSNE") ## ----eval = FALSE------------------------------------------------------------- # dataTrans <- # testData[, c("SYK", "CD16", "CD57", "EAT.2", "CD8", "NKG2C", "CD2", "CD56")] # # testData$groupProb <- groupProbPlot(xYData = testDataSNE$Y, # groupVector = testData$label, # groupName1 = "Group_1", # groupName2 = "Group_2", # dataTrans = dataTrans) # ## [1] "Done with k-means" # ## [1] "Now the first bit is done, and the iterative part takes off" # ## [1] "Clusters 1 to 7 smoothed in 2.9159369468689 . Now, 13 clusters are # ## [1] left." # ## [1] "Clusters 8 to 14 smoothed in 0.925199031829834 . Now, 6 clusters are # ## [1] left." # ## [1] "Clusters 15 to 20 smoothed in 0.905373096466064 . Now, 0 clusters are # ## [1] left." ## ----------------------------------------------------------------------------- sessionInfo()