scrna.sce <- as.SingleCellExperiment(scrna)
sce <- slingshot(scrna.sce, clusterLabels = "seurat_clusters", reducedDim = "PCA", approx_points = 100, start.clus = "1")
Using diagonal covariance matrix
Error in smooth.spline(lambda, xj, w = w, ..., df = df, tol = tol, keep.data = FALSE, : unused argument (approx_points = 100)
Traceback:
1. slingshot(scrna.sce, clusterLabels = "seurat_clusters", reducedDim = "PCA",
. approx_points = 100, start.clus = "1")
2. slingshot(scrna.sce, clusterLabels = "seurat_clusters", reducedDim = "PCA",
. approx_points = 100, start.clus = "1")
3. .local(data, clusterLabels, ...)
4. slingshot(data = rd, clusterLabels = cl, reducedDim = NULL, start.clus = start.clus,
. end.clus = end.clus, dist.fun = dist.fun, omega = omega,
. shrink = shrink, extend = extend, reweight = reweight, reassign = reassign,
. thresh = thresh, maxit = maxit, stretch = stretch, smoother = smoother,
. shrink.method = shrink.method, allow.breaks = allow.breaks,
. ...)
5. slingshot(data = rd, clusterLabels = cl, reducedDim = NULL, start.clus = start.clus,
. end.clus = end.clus, dist.fun = dist.fun, omega = omega,
. shrink = shrink, extend = extend, reweight = reweight, reassign = reassign,
. thresh = thresh, maxit = maxit, stretch = stretch, smoother = smoother,
. shrink.method = shrink.method, allow.breaks = allow.breaks,
. ...)
6. .local(data, clusterLabels, ...)
7. slingshot(data = data, clusterLabels = as.character(clusterLabels),
. reducedDim = reducedDim, start.clus = start.clus, end.clus = end.clus,
. dist.fun = dist.fun, omega = omega, shrink = shrink, extend = extend,
. reweight = reweight, reassign = reassign, thresh = thresh,
. maxit = maxit, stretch = stretch, smoother = smoother, shrink.method = shrink.method,
. allow.breaks = allow.breaks, ...)
8. slingshot(data = data, clusterLabels = as.character(clusterLabels),
. reducedDim = reducedDim, start.clus = start.clus, end.clus = end.clus,
. dist.fun = dist.fun, omega = omega, shrink = shrink, extend = extend,
. reweight = reweight, reassign = reassign, thresh = thresh,
. maxit = maxit, stretch = stretch, smoother = smoother, shrink.method = shrink.method,
. allow.breaks = allow.breaks, ...)
9. .local(data, clusterLabels, ...)
10. getCurves(sds, shrink = shrink, extend = extend, reweight = reweight,
. reassign = reassign, thresh = thresh, maxit = maxit, stretch = stretch,
. smoother = smoother, shrink.method = shrink.method, allow.breaks = allow.breaks,
. ...)
11. getCurves(sds, shrink = shrink, extend = extend, reweight = reweight,
. reassign = reassign, thresh = thresh, maxit = maxit, stretch = stretch,
. smoother = smoother, shrink.method = shrink.method, allow.breaks = allow.breaks,
. ...)
12. .local(sds, ...)
13. smootherFcn(pcurve$lambda, X[, jj], w = pcurve$w, ...)
14. tryCatch({
. smooth.spline(lambda, xj, w = w, ..., df = df, tol = tol,
. keep.data = FALSE)
. }, error = function(e) {
. smooth.spline(lambda, xj, w = w, ..., df = df, tol = tol,
. keep.data = FALSE, spar = 1)
. })
15. tryCatchList(expr, classes, parentenv, handlers)
16. tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. value[[3L]](cond)