first try rliger `runOnlineINMF`

liger.R

#install.packages('RcppPlanc', repos = c('https://welch-lab.r-universe.dev', 'https://cloud.r-project.org'))
library(rliger)
library(RcppPlanc)
library(bench)
pbmc <- normalize(pbmc)
pbmc <- selectGenes(pbmc)
pbmc <- scaleNotCenter(pbmc)
getOption("ligerVerbose", TRUE)

bm <-  bench::mark({
  pbmc <- runOnlineINMF(pbmc, k=20, nCores = 1,
                        minibatchSize = 200, maxEpochs = 10, 
                        verbose = FALSE)
}, iterations = 1)

print(bm$total_time)
#[1] 47.7ms
print(bm$mem_alloc)
#[1] 371KB

W = getMatrix(pbmc, slot = "W")
V = getMatrix(pbmc, slot = "V")
H = getMatrix(pbmc, slot = "H")

X = getMatrix(pbmc, slot = "scaleData")

dim(X$ctrl)
dim(X$stim)

#checking goodness-of-fit
plot((W + V$ctrl)%*%H$ctrl, X$ctrl, col=rgb(0, 0, 0, 0.1))
abline(0,1, col="royalblue", lty=2)
plot((W + V$stim)%*%H$stim, X$stim, col=rgb(0, 0, 0, 0.1))
abline(0,1, col="royalblue", lty=2)