Prepare for upcoming Seurat v5 release

[saketkc]

I am opening this issue as a notification because conos is listed here as a package that relies (depends/imports/suggests) on Seurat. As you may know, we recently released Seurat v5 as a beta in March of this year, with new updates for spatial, multimodal, and massively scalable analysis. For more information on updates and improvements, check out our website https://satijalab.org/seurat/.
We are now preparing to release Seurat v5 to CRAN, and plan to submit it on October 23rd. While we have tried our best to keep things backward-compatible, it is possible that updates to Seurat and SeuratObject might break your existing functionality or tests. We wanted to reach out before the new version is on CRAN, so that there's time to report issues/incompatibilities and prepare you for any changes in your code base that might be necessary.

We apologize for any disruption or inconvenience, but hope that the improvements to Seurat v5 will benefit your users going forward.
To test the upcoming release, you can install Seurat from the seurat5 branch using the instructions available on this page: https://satijalab.org/seurat/articles/install.

Thank you!
Seurat v5 team

[evanbiederstedt]

Hi @saketkc

Thanks for the heads up.

We basically try to check for various versions of Seurat:

conos/R/integrations.R

Lines 28 to 91 in 7cc6729

	#' @keywords internal
	checkSeuratV3 <- function() {
	if (!requireNamespace('Seurat', quietly = TRUE) || packageVersion('Seurat') < package_version(x = '3.0.0')) {
	stop("Use of Seurat v3-backed Conos objects requires Seurat v3.X installed")
	}
	}
	#' @keywords internal
	seuratProcV2 <- function(count.matrix, vars.to.regress=NULL, verbose=TRUE, do.par=TRUE, n.pcs=100, cluster=TRUE, tsne=TRUE, umap=FALSE) {
	if (!requireNamespace("Seurat", quietly = TRUE)) {
	stop("Package \"Seurat\" is needed for this function to work. Please install it, as described here: <https://satijalab.org/seurat/articles/install.html>.", call. = FALSE)
	}
	if (verbose) {
	message("Running Seurat v2 workflow")
	}
	rownames(count.matrix) <- make.unique(rownames(count.matrix))
	max.n.pcs <- min(nrow(count.matrix) - 1, ncol(count.matrix) - 1, n.pcs)
	so <- Seurat::CreateSeuratObject(count.matrix, display.progress=verbose) %>%
	Seurat::NormalizeData(display.progress=verbose) %>%
	Seurat::ScaleData(vars.to.regress=vars.to.regress, display.progress=verbose, do.par=do.par) %>%
	Seurat::FindVariableFeatures(do.plot = FALSE, display.progress=verbose) %>%
	Seurat::RunPCA(pcs.compute=max.n.pcs, do.print=FALSE)
	if (cluster) {
	so <- Seurat::FindClusters(so, n.iter=500, n.start=10, dims.use=1:n.pcs, print.output = FALSE)
	}
	if (tsne) {
	so <- Seurat::RunTSNE(so, dims.use=1:n.pcs)
	}
	if (umap) {
	if (packageVersion('Seurat') < package_version(x = '2.3.1')) {
	warning("UMAP support in Seurat came in v2.3.1, please update to a newer version of Seurt to enable UMAP functionality", immediate. = TRUE)
	} else {
	so <- Seurat::RunUMAP(object = so, dims.use = 1:n.pcs)
	}
	}
	return(so)
	}
	#' @keywords internal
	seuratProcV3 <- function(count.matrix, vars.to.regress=NULL, verbose=TRUE, n.pcs=100, cluster=TRUE, tsne=TRUE, umap=FALSE, ...) {
	if (!requireNamespace("Seurat", quietly = TRUE)) {
	stop("Package \"Seurat\" needed for this function to work. Please install it, as described here: <https://satijalab.org/seurat/articles/install.html>.", call. = FALSE)
	}
	if (verbose) {
	message("Running Seurat v3 workflow")
	}
	so <- Seurat::CreateSeuratObject(counts = count.matrix)
	so <- Seurat::NormalizeData(object = so, verbose = verbose)
	so <- Seurat::FindVariableFeatures(object = so, verbose = verbose)
	so <- Seurat::ScaleData(object = so, vars.to.regress = vars.to.regress, verbose = verbose)
	so <- Seurat::RunPCA(object = so, npcs = n.pcs, verbose = verbose)
	if (cluster) {
	so <- Seurat::FindNeighbors(object = so, dims = 1:n.pcs, verbose = verbose)
	so <- Seurat::FindClusters(object = so, n.iter = 500, n.start = 10, verbose = verbose)
	}
	if (tsne) {
	so <- Seurat::RunTSNE(object = so, dims = 1:n.pcs)
	}
	if (umap) {
	so <- Seurat::RunUMAP(object = so, dims = 1:n.pcs, verbose = verbose)
	}
	return(so)
	}

Given breaking changes for v5, would you be able to help out pointing out what needs to change?

If I have some pointers, I could do work here. But I don't have the bandwidth to check all edge cases right now.

Best, Evan