Can't run identifyClusters
f6v opened this issue · 4 comments
f6v commented
I've been trying to run scAI in an HPC environment. Here's the code:
LIB_PATH = "./R_libs/R-4.0.0/"
library(Seurat)
library(ggplot2)
library(scAI, lib.loc = LIB_PATH)
library(swne, lib.loc = LIB_PATH)
load("./data/data_simulation.rda")
X <- data_simulation$data
labels <- data_simulation$labels
scAI_outs <- create_scAIobject(raw.data = X, do.sparse = F)
cat("Preprocessing...")
scAI_outs <- preprocessing(scAI_outs, assay = NULL)
cat("Running scAI...")
scAI_outs <- run_scAI(scAI_outs, K = 20, nrun = 1, do.fast = T)
cat("Running identifyClusters...")
scAI_outs <- identifyClusters(scAI_outs, resolution = 0.9)
cat("Running getAggregatedData...")
scAI_outs <- getAggregatedData(scAI_outs, group = scAI_outs@identity)
cat("Running reducedDims...")
scAI_outs <- reducedDims(scAI_outs, method = "tsne")
cat("Running cellVisualization...")
umap_plot <- cellVisualization(scAI_outs, scAI_outs@embed$umap, color.by = "cluster")
ggsave("./results/umap_clusters.png", umap_plot)
I've tried both simulated and 10x PBMC dataset. Every time it fails on identifyClusters:
Error in `$<-.data.frame`(S3Part(x, TRUE), name, value) :
replacement has 500 rows, data has 0
Calls: identifyClusters -> $<- -> $<- -> $<-.data.frame
Would you have any advice?
f6v commented
Running interactively with traceback after error gives:
5: stop(sprintf(ngettext(N, "replacement has %d row, data has %d",
"replacement has %d rows, data has %d"), N, nrows), domain = NA)
4: `$<-.data.frame`(S3Part(x, TRUE), name, value)
3: `$<-`(`*tmp*`, "cluster", value = structure(c(1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 6L, 1L, 1L, 1L, 6L, 1L, 1L, 1L,
7L, 5L, 5L, 7L, 5L, 8L, 7L, 5L, 5L, 5L, 7L, 8L, 7L, 7L, 8L, 7L,
5L, 7L, 5L, 8L, 5L, 5L, 8L, 8L, 5L, 8L, 5L, 7L, 7L, 5L, 8L, 7L,
5L, 7L, 5L, 5L, 7L, 8L, 5L, 7L, 5L, 5L, 5L, 5L, 7L, 5L, 7L, 5L,
8L, 6L, 5L, 6L, 8L, 7L, 8L, 5L, 5L, 7L, 5L, 7L, 7L, 7L, 7L, 5L,
5L, 3L, 8L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 7L, 8L, 5L, 5L, 7L, 7L,
7L, 8L, 5L, 7L, 5L, 5L, 5L, 5L, 8L, 5L, 5L, 7L, 7L, 7L, 7L, 5L,
5L, 5L, 7L, 5L, 6L, 6L, 4L, 4L, 6L, 6L, 6L, 4L, 6L, 4L, 6L, 4L,
6L, 6L, 6L, 4L, 4L, 4L, 6L, 6L, 6L, 6L, 4L, 4L, 6L, 4L, 4L, 4L,
6L, 6L, 4L, 4L, 6L, 6L, 6L, 4L, 6L, 4L, 4L, 6L, 4L, 4L, 4L, 4L,
4L, 4L, 6L, 4L, 4L, 9L, 4L, 4L, 6L, 4L, 4L, 4L, 4L, 6L, 4L, 6L,
6L, 6L, 4L, 4L, 4L, 6L, 4L, 4L, 6L, 6L, 6L, 4L, 4L, 4L, 6L, 6L,
4L, 6L, 4L, 6L, 4L, 6L, 6L, 6L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 6L, 6L, 6L, 6L, 4L, 3L, 9L, 3L, 9L, 3L, 9L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 9L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 5L, 3L, 9L, 3L, 3L, 3L, 9L, 3L,
3L, 3L, 9L, 3L, 9L, 3L, 3L, 3L, 3L, 3L, 9L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 9L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 9L, 3L, 3L, 3L, 3L, 9L, 3L, 9L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 9L, 3L, 3L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 8L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 8L, 2L, 1L, 8L, 8L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L
), .Names = c(NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_), .Label = c("1", "2", "3", "4", "5", "6", "7",
"8", "9"), class = "factor"))
2: `$<-`(`*tmp*`, "cluster", value = structure(c(1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 6L, 1L, 1L, 1L, 6L, 1L, 1L, 1L,
7L, 5L, 5L, 7L, 5L, 8L, 7L, 5L, 5L, 5L, 7L, 8L, 7L, 7L, 8L, 7L,
5L, 7L, 5L, 8L, 5L, 5L, 8L, 8L, 5L, 8L, 5L, 7L, 7L, 5L, 8L, 7L,
5L, 7L, 5L, 5L, 7L, 8L, 5L, 7L, 5L, 5L, 5L, 5L, 7L, 5L, 7L, 5L,
8L, 6L, 5L, 6L, 8L, 7L, 8L, 5L, 5L, 7L, 5L, 7L, 7L, 7L, 7L, 5L,
5L, 3L, 8L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 7L, 8L, 5L, 5L, 7L, 7L,
7L, 8L, 5L, 7L, 5L, 5L, 5L, 5L, 8L, 5L, 5L, 7L, 7L, 7L, 7L, 5L,
5L, 5L, 7L, 5L, 6L, 6L, 4L, 4L, 6L, 6L, 6L, 4L, 6L, 4L, 6L, 4L,
6L, 6L, 6L, 4L, 4L, 4L, 6L, 6L, 6L, 6L, 4L, 4L, 6L, 4L, 4L, 4L,
6L, 6L, 4L, 4L, 6L, 6L, 6L, 4L, 6L, 4L, 4L, 6L, 4L, 4L, 4L, 4L,
4L, 4L, 6L, 4L, 4L, 9L, 4L, 4L, 6L, 4L, 4L, 4L, 4L, 6L, 4L, 6L,
6L, 6L, 4L, 4L, 4L, 6L, 4L, 4L, 6L, 6L, 6L, 4L, 4L, 4L, 6L, 6L,
4L, 6L, 4L, 6L, 4L, 6L, 6L, 6L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 6L, 6L, 6L, 6L, 4L, 3L, 9L, 3L, 9L, 3L, 9L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 9L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 5L, 3L, 9L, 3L, 3L, 3L, 9L, 3L,
3L, 3L, 9L, 3L, 9L, 3L, 3L, 3L, 3L, 3L, 9L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 9L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 9L, 3L, 3L, 3L, 3L, 9L, 3L, 9L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 9L, 3L, 3L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 8L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 8L, 2L, 1L, 8L, 8L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L
), .Names = c(NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_), .Label = c("1", "2", "3", "4", "5", "6", "7",
"8", "9"), class = "factor"))
f6v commented
The issue seems to arise when I don't add labels like:
scAI_outs <- addpData(scAI_outs, pdata = labels, pdata.name = "Cell types")
However, I'm a bit confused. Where do this labels come from? The simulated data works fine with labels, but I don't have them for the real dataset.
sqjin commented
Hi @f6v , The step addpData is optional. For simulated data, we just use the ground-truth labels to validate our results. For real dataset, you can simply skip it.
For the error you encountered, I am sorry I have no idea on it. When you run the simulated data in your local computer, do you have the similar issue?
f6v commented
@sqjin thanks for getting back to me!
I think the labels are in fact required: take this notebook as an example. If I remove the labels, it fails to run properly, with the same error I originally posted.
A wild guess would be that it fails around here, but I'm not at all familiar with the implementation.