## ----dsetup,echo=FALSE,results="hide",include=FALSE------------------------ suppressPackageStartupMessages({ library(BiocSklearn) library(BiocStyle) }) ## ----loadup---------------------------------------------------------------- library(BiocSklearn) skels = SklearnEls() skels ## ----doimp----------------------------------------------------------------- irloc = system.file("csv/iris.csv", package="BiocSklearn") irismat = skels$np$genfromtxt(irloc, delimiter=',') ## ----dota------------------------------------------------------------------ skels$np$take(irismat, 0:2, 0L ) ## ----dor------------------------------------------------------------------- fullpc = prcomp(data.matrix(iris[,1:4]))$x ## ----dopc1----------------------------------------------------------------- ppca = skPCA(irismat) ppca ## ----lk1------------------------------------------------------------------- tx = getTransformed(ppca) dim(tx) head(tx) ## ----dopy------------------------------------------------------------------ pyobj(ppca)$fit_transform(irismat)[1:3,] ## ----lkconc---------------------------------------------------------------- round(cor(tx, fullpc),3) ## ----doincr---------------------------------------------------------------- ippca = skIncrPCA(irismat) # ippcab = skIncrPCA(irismat, batch_size=25L) round(cor(getTransformed(ippcab), fullpc),3) ## ----dopartial------------------------------------------------------------- ta = skels$np$take # provide slicer utility ipc = skPartialPCA_step(ta(irismat,0:49,0L)) ipc = skPartialPCA_step(ta(irismat,50:99,0L), obj=ipc) ipc = skPartialPCA_step(ta(irismat,100:149,0L), obj=ipc) ipc$transform(ta(irismat,0:5,0L)) fullpc[1:5,] ## ----lkmref---------------------------------------------------------------- fn = system.file("ban_6_17/assays.h5", package="BiocSklearn") ban = H5matref(fn) ban ## ----getmmm---------------------------------------------------------------- np = import("numpy", convert=FALSE) # ensure ban$shape ## ----dotx------------------------------------------------------------------ ban2 = np$matrix(ban)$T ## ----dopart---------------------------------------------------------------- st = skPartialPCA_step(ta(ban2, 0:999, 0L)) st = skPartialPCA_step(ta(ban2, 1000:10999, 0L), obj=st) st = skPartialPCA_step(ta(ban2, 11000:44559, 0L), obj=st) sss = st$transform(ban2) ## ----dover----------------------------------------------------------------- iii = skPCA(ban2) dim(getTransformed(iii)) round(cor(sss[,1:4], getTransformed(iii)[,1:4]),3)