cole-trapnell-lab
Error in graph_test function
Hi!
When I run the following code: ciliated_cds_pr_test_res <- graph_test(cds, neighbor_graph="principal_graph", reduction_method="UMAP", cores=4)
I get this error: Error: 'rBind' is defunct. Since R version 3.2.0, base's rbind() should work fine with S4 objects Traceback:
- graph_test(cds, neighbor_graph = "principal_graph", reduction_method = "UMAP", . cores = 4)
- calculateLW(cds, k = k, verbose = verbose, neighbor_graph = neighbor_graph, . reduction_method = reduction_method)
- Matrix::rBind(tmp, cur_tmp)
- .Defunct(msg = "'rBind' is defunct.\n Since R version 3.2.0, base's rbind() should work fine with S4 objects")
If I run the graph_test function with knn as neighbor_graph it works, but I would rather use principal_graph.
I'm also waiting for the author's fixes on this. This issue can be followed up here: #512
Here is the message I have, but it look a little different from the error messages that other people posted.
Warning message:
“'rBind' is deprecated.
Since R version 3.2.0, base's rbind() should work fine with S4 objects”
|=======================================================| 100%, Elapsed 12:19
Error in (function (..., deparse.level = 1, make.row.names = TRUE, stringsAsFactors = default.stringsAsFactors(), : invalid list argument: all variables should have the same length
Traceback:
1. graph_test(par1, neighbor_graph = "principal_graph", cores = 1)
2. do.call(rbind.data.frame, test_res)
3. (function (..., deparse.level = 1, make.row.names = TRUE, stringsAsFactors = default.stringsAsFactors(),
. factor.exclude = TRUE)
. {
. match.names <- function(clabs, nmi) {
. if (identical(clabs, nmi))
. NULL
. else if (length(nmi) == length(clabs) && all(nmi %in%
. clabs)) {
. m <- pmatch(nmi, clabs, 0L)
. if (any(m == 0L))
. stop("names do not match previous names")
. m
. }
. else stop("names do not match previous names")
. }
. allargs <- list(...)
. allargs <- allargs[lengths(allargs) > 0L]
. if (length(allargs)) {
. nr <- vapply(allargs, function(x) if (is.data.frame(x))
. .row_names_info(x, 2L)
. else if (is.list(x))
. length(x[[1L]])
. else length(x), 1L)
. if (any(n0 <- nr == 0L)) {
. if (all(n0))
. return(allargs[[1L]])
. allargs <- allargs[!n0]
. }
. }
. n <- length(allargs)
. if (n == 0L)
. return(list2DF())
. nms <- names(allargs)
. if (is.null(nms))
. nms <- character(n)
. cl <- NULL
. perm <- rows <- vector("list", n)
. if (make.row.names) {
. rlabs <- rows
. autoRnms <- TRUE
. Make.row.names <- function(nmi, ri, ni, nrow) {
. if (nzchar(nmi)) {
. if (autoRnms)
. autoRnms <<- FALSE
. if (ni == 0L)
. character()
. else if (ni > 1L)
. paste(nmi, ri, sep = ".")
. else nmi
. }
. else if (autoRnms && nrow > 0L && identical(ri, seq_len(ni)))
. as.integer(seq.int(from = nrow + 1L, length.out = ni))
. else {
. if (autoRnms && (nrow > 0L || !identical(ri,
. seq_len(ni))))
. autoRnms <<- FALSE
. ri
. }
. }
. }
. smartX <- isTRUE(factor.exclude)
. nrow <- 0L
. value <- clabs <- NULL
. all.levs <- list()
. for (i in seq_len(n)) {
. xi <- allargs[[i]]
. nmi <- nms[i]
. if (is.matrix(xi))
. allargs[[i]] <- xi <- as.data.frame(xi, stringsAsFactors = stringsAsFactors)
. if (inherits(xi, "data.frame")) {
. if (is.null(cl))
. cl <- oldClass(xi)
. ri <- attr(xi, "row.names")
. ni <- length(ri)
. if (is.null(clabs))
. clabs <- names(xi)
. else {
. if (length(xi) != length(clabs))
. stop("numbers of columns of arguments do not match")
. pi <- match.names(clabs, names(xi))
. if (!is.null(pi))
. perm[[i]] <- pi
. }
. rows[[i]] <- seq.int(from = nrow + 1L, length.out = ni)
. if (make.row.names)
. rlabs[[i]] <- Make.row.names(nmi, ri, ni, nrow)
. nrow <- nrow + ni
. if (is.null(value)) {
. value <- unclass(xi)
. nvar <- length(value)
. all.levs <- vector("list", nvar)
. has.dim <- facCol <- ordCol <- logical(nvar)
. if (smartX)
. NA.lev <- ordCol
. for (j in seq_len(nvar)) {
. xj <- value[[j]]
. facCol[j] <- fac <- if (!is.null(lj <- levels(xj))) {
. all.levs[[j]] <- lj
. TRUE
. }
. else is.factor(xj)
. if (fac) {
. ordCol[j] <- is.ordered(xj)
. if (smartX && !NA.lev[j])
. NA.lev[j] <- anyNA(lj)
. }
. has.dim[j] <- length(dim(xj)) == 2L
. }
. }
. else for (j in seq_len(nvar)) {
. xij <- xi[[j]]
. if (is.null(pi) || is.na(jj <- pi[[j]]))
. jj <- j
. if (facCol[jj]) {
. if (length(lij <- levels(xij))) {
. all.levs[[jj]] <- unique(c(all.levs[[jj]],
. lij))
. if (ordCol[jj])
. ordCol[jj] <- is.ordered(xij)
. if (smartX && !NA.lev[jj])
. NA.lev[jj] <- anyNA(lij)
. }
. else if (is.character(xij))
. all.levs[[jj]] <- unique(c(all.levs[[jj]],
. xij))
. }
. }
. }
. else if (is.list(xi)) {
. ni <- range(lengths(xi))
. if (ni[1L] == ni[2L])
. ni <- ni[1L]
. else stop("invalid list argument: all variables should have the same length")
. rows[[i]] <- ri <- as.integer(seq.int(from = nrow +
. 1L, length.out = ni))
. nrow <- nrow + ni
. if (make.row.names)
. rlabs[[i]] <- Make.row.names(nmi, ri, ni, nrow)
. if (length(nmi <- names(xi)) > 0L) {
. if (is.null(clabs))
. clabs <- nmi
. else {
. if (length(xi) != length(clabs))
. stop("numbers of columns of arguments do not match")
. pi <- match.names(clabs, nmi)
. if (!is.null(pi))
. perm[[i]] <- pi
. }
. }
. }
. else if (length(xi)) {
. rows[[i]] <- nrow <- nrow + 1L
. if (make.row.names)
. rlabs[[i]] <- if (nzchar(nmi))
. nmi
. else as.integer(nrow)
. }
. }
. nvar <- length(clabs)
. if (nvar == 0L)
. nvar <- max(lengths(allargs))
. if (nvar == 0L)
. return(list2DF())
. pseq <- seq_len(nvar)
. if (is.null(value)) {
. value <- list()
. value[pseq] <- list(logical(nrow))
. all.levs <- vector("list", nvar)
. has.dim <- facCol <- ordCol <- logical(nvar)
. if (smartX)
. NA.lev <- ordCol
. }
. names(value) <- clabs
. for (j in pseq) if (length(lij <- all.levs[[j]]))
. value[[j]] <- factor(as.vector(value[[j]]), levels = lij,
. exclude = if (smartX) {
. if (!NA.lev[j])
. NA
. }
. else factor.exclude, ordered = ordCol[j])
. if (any(has.dim)) {
. jdim <- pseq[has.dim]
. if (!all(df <- vapply(jdim, function(j) inherits(value[[j]],
. "data.frame"), NA))) {
. rmax <- max(unlist(rows))
. for (j in jdim[!df]) {
. dn <- dimnames(vj <- value[[j]])
. rn <- dn[[1L]]
. if (length(rn) > 0L)
. length(rn) <- rmax
. pj <- dim(vj)[2L]
. length(vj) <- rmax * pj
. value[[j]] <- array(vj, c(rmax, pj), list(rn,
. dn[[2L]]))
. }
. }
. }
. for (i in seq_len(n)) {
. xi <- unclass(allargs[[i]])
. if (!is.list(xi))
. if (length(xi) != nvar)
. xi <- rep(xi, length.out = nvar)
. ri <- rows[[i]]
. pi <- perm[[i]]
. if (is.null(pi))
. pi <- pseq
. for (j in pseq) {
. jj <- pi[j]
. xij <- xi[[j]]
. if (has.dim[jj]) {
. value[[jj]][ri, ] <- xij
. if (!is.null(r <- rownames(xij)) && !(inherits(xij,
. "data.frame") && .row_names_info(xij) <= 0))
. rownames(value[[jj]])[ri] <- r
. }
. else {
. value[[jj]][ri] <- if (is.factor(xij))
. as.vector(xij)
. else xij
. if (!is.null(nm <- names(xij)))
. names(value[[jj]])[ri] <- nm
. }
. }
. }
. rlabs <- if (make.row.names && !autoRnms) {
. rlabs <- unlist(rlabs)
. if (anyDuplicated(rlabs))
. make.unique(as.character(rlabs), sep = "")
. else rlabs
. }
. if (is.null(cl)) {
. as.data.frame(value, row.names = rlabs, fix.empty.names = TRUE,
. stringsAsFactors = stringsAsFactors)
. }
. else {
. structure(value, class = cl, row.names = if (is.null(rlabs))
. .set_row_names(nrow)
. else rlabs)
. }
. })(value = list(structure(list(status = "FAIL", p_value = NA,
. morans_test_statistic = NA, morans_I = NA), class = "data.frame", row.names = c(NA,
. -1L)), structure(list(status = "FAIL", p_value = NA, morans_test_statistic = NA,
. morans_I = NA), class = "data.frame", row.names = c(NA, -1L
. )),
... (repeats many times)...
structure(list(status = "FAIL", p_value = NA, morans_test_statistic = NA,
. morans_I = NA), class = "data.frame", row.names = c(NA, -1L
. ))), warning = structure(list(message = "NaNs produced", call = FUN(...)), class = c("simpleWarning",
. "warning", "condition")))
4. stop("invalid list argument: all variables should have the same length")
Hi,
I tried running graph_test and I get this error:
Error in (function (..., deparse.level = 1, make.row.names = TRUE, stringsAsFactors = FALSE, : invalid list argument: all variables should have the same length
Code: `cds <- estimate_size_factors(cds)
Add gene names into CDS
cds@rowRanges@elementMetadata@listData[["gene_short_name"]] <- rownames(sobj[["RNA"]])
deg <- graph_test(cds, neighbor_graph = "principal_graph") deg %>% arrange(q_value) %>% filter(status == "OK") %>% head()`
Could you help in figuring out?
Thank you!
@apal6 I'm having this same issue with graph_test. did you ever find a fix for it?
@substantia-nigra Yes, I was able to fix this.
I think re running the fdata(cds) solved the error. Also updated my packages. Hope this helps.
`#LOAD THE OBJECT
cds <- SeuratWrappers::as.cell_data_set(seurat_obj) head(colData(cds)) fData(cds) rownames(fData(cds))[1:10] fData(cds)$gene_short_name <- rownames(fData(cds))
head(fData(cds)) head(counts(cds))
recreate.partitions <- c(rep(1, length(cds@colData@rownames))) names(recreate.partitions) <- cds@colData@rownames recreate.partitions <- as.factor(recreate.partitions) recreate.partitions
cds@clusters@listData[["UMAP"]][["partitions"]] <- recreate.partitions
list.cluster <[email protected] cds@clusters@listData[["UMAP"]][["clusters"]] <- list.cluster
cds@int_colData@listData[["reducedDims"]]@listData[["UMAP"]] <-seurat_obj@[email protected]
cds <- learn_graph(cds, use_partition = F) cds <- order_cells(cds, reduction_method = "UMAP", root_cells = colnames(cds[, clusters(cds) == "CD8-TPex"]))
head(pseudotime(cds), 10) cds$monocle3_pseudotime <- pseudotime(cds) data.pseudo <- as.data.frame(colData(cds))
#cds <- monocle3::estimate_size_factors(cds)
Add gene names into CDS
#cds@rowRanges@elementMetadata@listData[["gene_short_name"]] <-#rownames(seurat_obj[["RNA"]])
#If this gives an error: rerun the fdata(cds) code and then run this
#fData(cds) #rownames(fData(cds))[1:10] #fData(cds)$gene_short_name <- rownames(fData(cds)) #head(fData(cds)) #head(counts(cds))
deg <- graph_test(cds, neighbor_graph = "principal_graph", cores=8) top_genes <- deg %>% arrange(q_value) %>% dplyr::filter(status == "OK")`