#Angle plot
microbenchmark({
data(iris)
iris$group <- "setosa"
iris$group[iris$Species != "setosa"] <- "non-setosa"
irisPCADSC <- PCADSC(iris, "group", setdiff(names(iris), c("group", "Species")))
irisPCADSC2 <- PCADSC(iris, "group", setdiff(names(iris), c("group", "Species")), doAngle = FALSE)
irisPCADSC2 <- doAngle(irisPCADSC2)
anglePlot(irisPCADSC)
anglePlot(irisPCADSC2)
}, times = 10)
#min lq mean median uq max neval
#4.061592 4.085913 4.364346 4.210754 4.329815 5.858282 10
#CE plot
microbenchmark({
data(iris)
iris$group <- "setosa"
iris$group[iris$Species != "setosa"] <- "non-setosa"
irisPCADSC <- PCADSC(iris, "group", setdiff(names(iris), c("group", "Species")))
irisPCADSC2 <- PCADSC(iris, "group", setdiff(names(iris), c("group", "Species")),
doCE = FALSE)
irisPCADSC2 <- doCE(irisPCADSC2)
CEPlot(irisPCADSC)
CEPlot(irisPCADSC2)
}, times = 10)
#min lq mean median uq max neval
#3.612281 3.70354 3.852662 3.841499 3.892452 4.158875 10
#Chroma plot
microbenchmark({
data(iris)
iris$group <- "setosa"
iris$group[iris$Species != "setosa"] <- "non-setosa"
irisPCADSC <- PCADSC(iris, "group", setdiff(names(iris), c("group", "Species")))
irisPCADSC2 <- PCADSC(iris, "group", setdiff(names(iris), c("group", "Species")),
doChroma = FALSE)
irisPCADSC2 <- doChroma(irisPCADSC2)
chromaPlot(irisPCADSC)
chromaPlot(irisPCADSC)
chromaPlot(irisPCADSC, splitLabels = list("non-setosa" = "Not Setosa",
"setosa" = "Setosa"))
chromaPlot(irisPCADSC, useComps = c(1,4), varAnnotation = "no")
chromaPlot(irisPCADSC, cvCO = 0.8)
chromaPlot(irisPCADSC, varLabels = c("Sepal length", "Sepal width", "Petal length",
"Petal width"))
})
#do Angle
microbenchmark({
#' #load iris data
#' data(iris)
#'
#' #Define grouping variable, grouping the observations by whether their species is
#' #Setosa or not
#' iris$group <- "setosa"
#' iris$group[iris$Species != "setosa"] <- "non-setosa"
#'
#' #make a partial PCADSC object, splitting the data by "group"
#' irisPCADSC <- PCADSC(iris, "group", setdiff(names(iris), c("group", "Species")),
#' doAngle = FALSE)
#'
#' #No angleInfo available
#' irisPCADSC$angleInfo
#'
#' #Add and show angleInfo
#' irisPCADSC <- doAngle(irisPCADSC)
#' irisPCADSC$angleInfo
#' }
#'
})
#doCE
microbenchmark({
#' #load iris data
#' data(iris)
#'
#' #Define grouping variable, grouping the observations by whether their species is
#' #Setosa or not
#' iris$group <- "setosa"
#' iris$group[iris$Species != "setosa"] <- "non-setosa"
#'
#' #make a partial PCADSC object, splitting the data by "group"
#' irisPCADSC <- PCADSC(iris, "group", setdiff(names(iris), c("group", "Species")),
#' doCE = FALSE)
#'
#' #No CEInfo available
#' irisPCADSC$CEInfo
#'
#' #Add and show CEInfo
#' irisPCADSC <- doCE(irisPCADSC)
#' irisPCADSC$CEInfo
#' }
#'
})
#doChroma
microbenchmark({
#' #load iris data
#' data(iris)
#'
#' #Define grouping variable, grouping the observations by whether their species is
#' #Setosa or not
#' iris$group <- "setosa"
#' iris$group[iris$Species != "setosa"] <- "non-setosa"
#'
#' #make a partial PCADSC object, splitting the data by "group"
#' irisPCADSC <- PCADSC(iris, "group", setdiff(names(iris), c("group", "Species")),
#' doChroma = FALSE)
#'
#' #No chromaInfo available
#' irisPCADSC$chromaInfo
#'
#' #Add and show chromaInfo
#' irisPCADSC <- doChroma(irisPCADSC)
#' irisPCADSC$chromaInfo
#' }
#'
})
#PCADSC
microbenchmark({
#' #load iris data
#' data(iris)
#'
#' #Define grouping variable, grouping the observations by whether their species is
#' #Setosa or not
#' iris$group <- "setosa"
#' iris$group[iris$Species != "setosa"] <- "non-setosa"
#'
#' #Make a full PCADSC object, splitting the data by "group"
#' irisPCADSC <- PCADSC(iris, "group", setdiff(names(iris), c("group", "Species")))
#'
#' #The three plotting functions can now be called on irisPCADSC:
#' CEPlot(irisPCADSC)
#' anglePlot(irisPCADSC)
#' chromaPlot(irisPCADSC)
#'
#' #Make a partial PCADSC object with no angle plot information and add
#' #angle plot information afterwards:
#' irisPCADSC2 <- PCADSC(iris, "group", setdiff(names(iris), c("group", "Species")),
#' doAngle = FALSE)
#' irisPCADSC2 <- doAngle(irisPCADSC)
#' }
})
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