inst/doc/GroupProbPlot_usage.R

In DepecheR: Determination of essential phenotypic elements of clusters in high-dimensional entities

## ----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()