## ----doe44,message=FALSE------------------------------------------------------
library(scviR)
HDP.h5 = cacheCiteseqHDPdata()
mdata1 = muonR()$read_10x_h5(HDP.h5)
mdata1$mod["rna"]$var_names_make_unique()
reticulate::py_run_string('r.mdata1.mod["rna"].layers["counts"] = r.mdata1.mod["rna"].X.copy()')
mdata1

## ----doscanpy-----------------------------------------------------------------
scr = scanpyR()
scr$pp$normalize_total(mdata1$mod["rna"])
scr$pp$log1p(mdata1$mod["rna"])
#
scr$pp$highly_variable_genes(
    mdata1$mod["rna"],
    n_top_genes=4000L,
    flavor="seurat_v3",
    layer="counts",
)

## ----domu---------------------------------------------------------------------
reticulate::py_run_string('r.mdata1.mod["rna_subset"] = r.mdata1.mod["rna"][:, r.mdata1.mod["rna"].var["highly_variable"]].copy()')
mdata1 = MuDataR()$MuData(mdata1$mod)

## ----densify------------------------------------------------------------------
reticulate::py_run_string('r.mdata1["prot"].X = r.mdata1["prot"].X.toarray()')
reticulate::py_run_string('r.mdata1["rna_subset"].X = r.mdata1["rna_subset"].X.toarray()')
reticulate::py_run_string('r.mdata1.mod["rna_subset"].layers["counts"] = r.mdata1.mod["rna_subset"].layers["counts"].toarray()')
mdata1$update()

## ----dosetup------------------------------------------------------------------
scviR()$model$TOTALVI$setup_mudata(
    mdata1,
    rna_layer="counts",
    protein_layer=reticulate::py_none(),
    modalities=list(
        "rna_layer"= "rna_subset",
        "protein_layer"= "prot",
        "batch_key"= "rna_subset"
    ), 
)

## ----what---------------------------------------------------------------------
model = scviR()$model$TOTALVI(mdata1)
model

## ----dotrain, message=FALSE, results="hide"-----------------------------------
n_epochs = 50L
n_epochs.cpu = 5L
acc = "cpu"
tchk = try(reticulate::import("torch"))
if (!inherits(tchk, "try-error") && tchk$backends$mps$is_available()) acc = "mps"
if (!inherits(tchk, "try-error") && tchk$cuda$is_available()) acc = "gpu"
#runtim.cpu = system.time(model$train(max_epochs=n_epochs.cpu, accelerator = "cpu"))
runtim.cpu = c(NA,NA,NA)
runtim = system.time(model$train(max_epochs=n_epochs, accelerator = acc))

## ----lkelb--------------------------------------------------------------------
total_ep = n_epochs # + n_epochs.cpu
val_elbo = unlist(model$history$elbo_validation) 
tr_elbo = model$history$elbo_train$elbo_trai
plot(1:total_ep, tr_elbo, type="l", xlab="epoch", ylab="ELBO", ylim=c(0,7000))
lines(1:total_ep, val_elbo, col="blue")
legend(3, 6000, col=c("black", "blue"), lty=1, legend=c("train", "validate"))

## ----sessinf------------------------------------------------------------------
sessionInfo()