Error in STEP 15 during CNV analysis：plot_cnv(): auto thresholding at: (NA , NA)

[Duiduipeng]

This is the code for my run：
gene_order=read.table("F:/Rtest0924/Filered2 Data/inferCNV/hg38_gencode_v27.txt", row.names = 1)
MergeData<-readRDS("F:/Rtest0924/Filered2 Data/celltype.rds")
counts <- GetAssayData(MergeData, slot = 'counts')
Idents(MergeData) <- MergeData$celltype
sc_Merge <- subset(MergeData, idents = c(
"Fibroblast",
"Schwann Cell",
"T cell",
"Endothelium",
"Neuroendocrine-Related Cells",
"CAF",
"Smooth Muscle Cells",
"MPS",
"Adipocytes",
"T/NK"
))
reference_celltypes <- c("T cell", "MPS", "T/NK")
target_celltypes <- c("Neuroendocrine-Related Cells","Fibroblast", "Schwann Cell", "Endothelium", "CAF",
"Smooth Muscle Cells", "Adipocytes")
reference_cells <- row.names([email protected])[[email protected]$celltype %in% reference_celltypes]
target_cells <- row.names([email protected])[[email protected]$celltype %in% target_celltypes]
cells <- append(reference_cells, target_cells)
sc=subset(sc_Merge, cells=cells)
Anno=[email protected][,c("cellname","celltype")]
Anno$celltype=as.character(Anno$celltype)

Anno[is.na(Anno$seurat_clusters),3]=Anno[is.na(Anno$seurat_clusters),2]

rownames(Anno)=Anno$cellname
Anno=as.matrix(Anno)
ref_group_names = c(reference_cells, target_cells)
Anno=Anno%>% as.data.frame()
infercnv_sc = CreateInfercnvObject(raw_counts_matrix = counts,
annotations_file = Anno,
delim="\t",
gene_order_file = gene_order,
ref_group_names =ref_group_names)
infercnv_sc = infercnv::run(infercnv_sc,
cutoff=1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics
out_dir="F:/Rtest0924/Filered2 Data/inferCNV",
cluster_by_groups=TRUE,
denoise=FALSE,
HMM=FALSE,
write_expr_matrix=T,
output_format = "pdf")
This is an error：
INFO [2025-01-04 14:53:14] ::plot_cnv:Start
INFO [2025-01-04 14:53:14] ::plot_cnv:Current data dimensions (r,c)=9028,8123 Total=73334444 Min=1 Max=1.
INFO [2025-01-04 14:53:14] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2025-01-04 14:53:14] plot_cnv(): auto thresholding at: (NA , NA)
错误于seq.default(x.range[1], x.range[2], length.out = nb_breaks):
'from' must be a finite number
此外: 警告信息:
In max(nchar(obs_annotations_names)) : max里所有的参数都不存在；返回-Inf
debug finds that the error is in the source code:
plot_cnv(infercnv_obj, k_obs_groups = k_obs_groups,
cluster_by_groups = cluster_by_groups, cluster_references = cluster_references,
plot_chr_scale = plot_chr_scale, chr_lengths = chr_lengths,
out_dir = out_dir, x.center = final_center_val,
x.range = final_scale_limits, title = "inferCNV",
output_filename = "infercnv", output_format = output_format,
write_expr_matrix = write_expr_matrix, write_phylo = write_phylo,
png_res = png_res, useRaster = useRaster)
}
May I ask what is the reason for the error? What can I do about it?