Q: possible to simulate group-specific cde?

[HelenaLC]

Quick Q. We're using splatter to simulate 3 vs. 3 samples from 2 conditions, 3 clusters. However, it seems condition-differences cde are introduced "global"ly, i.e., all the same for every de group. Any way we could alter this? E.g., have cde only affect one group?

I tried simulating clusters independently with fixed seed, which let's me control cde. However, this kills any de between clusters, so it won't do... exemplary PCs and corresponding code below.

Hope that makes sense & happy to clarify if not. Cheers!!

seed <- 241122
t <- 1.5; s <- 2; b <- 0

vcf <- mockVCF(n.samples=6, seed=seed)
gff <- mockGFF(n.genes=800, seed=seed)

# simulate 'Group's = clusters in a loop
lys <- lapply(seq(3), \(.) {
    # set 'cde.facLoc=s' = condition effect
    # in all but one 'Group' = cluster
    if (. != 1) s <- 0 
    set.seed(seed)
    # simulate w/o DE effects
    p <- newSplatPopParams(
        # type
        #de.facLoc=t,
        #de.prob=0.1,
        #de.facScale=0.1*t,
        # state
        cde.prob=0.1,
        cde.facLoc=s,
        cde.facScale=0.1,
        bcv.common=1.5,
        batchCells=50,
        eqtl.ES.rate=30,
        similarity.scale=15,
        #group.prob=rep(1/3, 3), # cluster
        condition.prob=c(0.5, 0.5)) # condition
    
    # multiply overall 'lib.loc' by 1+'t' = cluster effect
    # (now clusters are always the same, though...?)
    # (and changing this would affect all genes...?)
    attr(p, ll) <- attr(p, ll <- "lib.loc")*(1+t)
    
    sim <- splatPopSimulate(
        params=p, vcf=vcf, gff=gff,
        verbose=FALSE, sparsify=FALSE)
    sim$Group <- letters[.]
    return(sim)
})

tmp <- lapply(lys, \(.) {
    rowData(.) <- NULL
    .
})
x <- do.call(cbind, tmp)
colData(x) <- DataFrame(
    cluster_id=x$Group,
    sample_id=x$Sample,
    group_id=x$Condition)

[lazappi]

Hi @HelenaLC

Thanks for giving {splatter} a go! As this relates to splatPop I'm hoping @azodichr can jump in with an answer. If not I'll try to look into it but it will take me a bit to get my head around how it works again.