Fail to make any visual results(.png)

[Geryxu08]

Hello! I work with infercnv version 1.6.0 in R(4.0.4) and I had a problem with the output result. I found that there are no any visual results(.png) which are completely empty.

• my raw_counts_matrix is from Seurat object(after sample integration) which of sample origin is Hepatocellular carcinoma in rat.
• my annotation_file is a tabbed table with two columns, one for cell barcode and the other for annotation information.
• my gene_order_file is a tabbed table with four columns, one for gene symbol, two for chromosome number, and the other for Starting position and ending position

Here's the code I ran: ` infercnv_obj = CreateInfercnvObject(raw_counts_matrix=matrix, annotations_file="cell_annotation3.txt", delim="\t", gene_order_file="gene_mouse.txt", ref_group_names=c('Endothelial cells','Dendritic cells'))

perform infercnv operations to reveal cnv signal

infercnv_obj = infercnv::run(infercnv_obj, cutoff=0.1,
out_dir="/share/inferCNV/",
cluster_by_groups=TRUE,
denoise=F, HMM=F) ` I wonder what is the reason for the lack of any visual results. Your help is highly appreciated! Thank you.

[GeorgescuC]

Hi @Geryxu08 ,

Based on the file sizes in the folder, there is data to plot so the code you ran is probably not the issue here. What OS are you running this on? Are you running this on a server? If you try to generate any other test plot to a png, does it plot properly?

Regards, Christophe.