Nothing
## ----set-options,echo=FALSE---------------------------------------------------
options(width=80)
knitr::opts_chunk$set(fig.align = 'center', out.width = '70%')
## ---- warning = FALSE---------------------------------------------------------
library(bigMap)
## ---- eval = TRUE, echo = FALSE, results = 'hide'-----------------------------
bdm.local('cluster-ceab.ceab.csic.es')
bdm.mybdm('~/myPath/')
## -----------------------------------------------------------------------------
bdm.example()
## ---- echo = FALSE------------------------------------------------------------
dMap.copy <- exMap$dMap
exMap$dMap <- NULL
## -----------------------------------------------------------------------------
str(exMap)
## -----------------------------------------------------------------------------
X <- exMap$data # let's assume this is our raw data matrix
dim(X)
## -----------------------------------------------------------------------------
myMap <- bdm.init('myDataset', X)
str(myMap)
## ---- eval = FALSE------------------------------------------------------------
# myDistMap <- bdm.init('myDataset', X, is.distance = TRUE) # don't run
## -----------------------------------------------------------------------------
L <- exMap$lbls # assume this is our vector of labels
## -----------------------------------------------------------------------------
myMap <- bdm.init('myDataset', X, labels = L)
str(myMap)
## ---- echo = FALSE------------------------------------------------------------
myMap$Xdata <- exMap$Xdata
myMap$Xbeta <- exMap$Xbeta
myMap$ptsne <- exMap$ptsne
## ---- eval = FALSE------------------------------------------------------------
# myMap <- bdm.ptsne(myMap, threads = 4, layers = 2, rounds = 2, ppx = 25)
## -----------------------------------------------------------------------------
str(myMap$ptsne)
## ---- fig.height = 4.0--------------------------------------------------------
bdm.ptsne.plot(myMap)
## ---- echo = FALSE------------------------------------------------------------
myMap$pakde <- exMap$pakde
myMap$pakde[[2]] <- NULL
## ---- eval = FALSE------------------------------------------------------------
# myMap <- bdm.pakde(myMap, threads = 4, ppx = 50, g.exp = 2)
## -----------------------------------------------------------------------------
str(myMap$pakde)
## ---- fig.height = 4.0--------------------------------------------------------
bdm.pakde.plot(myMap)
## ---- echo = FALSE------------------------------------------------------------
myMap$wtt <- exMap$wtt
myMap$wtt[[2]] <- NULL
## ---- eval = FALSE------------------------------------------------------------
# myMap <- bdm.wtt(myMap)
## -----------------------------------------------------------------------------
str(myMap$wtt)
## -----------------------------------------------------------------------------
bdm.wtt.plot(myMap)
## -----------------------------------------------------------------------------
myDataLabels <- bdm.labels(myMap)
## ---- fig.height = 3.8--------------------------------------------------------
bdm.cost(myMap)
## ---- fig.height = 3.5--------------------------------------------------------
bdm.ptsne.plot(myMap, ptsne.cex = 0.6, class.pltt = rainbow(16), layer = 2)
## ---- fig.height = 7.0--------------------------------------------------------
bdm.qMap(myMap, data = myMap$data[, 1:4], subset = which(myMap$lbls %in% 1:8))
## -----------------------------------------------------------------------------
# assume these are our class covariates
myclasses <- c('A', 'B', 'C', 'D', 'E')[(myMap$lbls %/% 4) +1]
## ---- echo = FALSE------------------------------------------------------------
myMap$dMap <- dMap.copy
## ---- eval = FALSE------------------------------------------------------------
# myMap <- bdm.dMap(myMap, threads = 4, data = myclasses)
## ---- fig.height = 6.0--------------------------------------------------------
bdm.dMap.plot(myMap, classes = c('A', 'B', 'E'))
## ---- fig.height = 5.5--------------------------------------------------------
bdm.boxp(myMap)
## ---- results = 'hide'--------------------------------------------------------
myMap <- bdm.optk.s2nr(myMap, plot.optk = F, ret.optk = T)
## ---- fig.height = 5.0--------------------------------------------------------
bdm.optk.plot(myMap)
## -----------------------------------------------------------------------------
myMap <- bdm.merge.s2nr(myMap, k = 6, plot.merge = F, ret.merge = T)
## ---- fig.height = 6.0--------------------------------------------------------
bdm.wtt.plot(myMap)
## -----------------------------------------------------------------------------
bdm.mybdm('~/myPath/')
## -----------------------------------------------------------------------------
bdm.fName(myMap)
## ---- eval = FALSE------------------------------------------------------------
# bdm.save(myMap)
## -----------------------------------------------------------------------------
bdm.local('xxx.xxx.xxx.xxx')
## ---- eval = FALSE------------------------------------------------------------
# bdm.scp(myMap)
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