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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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plot_cnv error #612

Open lvliang418 opened 10 months ago

lvliang418 commented 10 months ago

Hi all, I'm trying to use the final infercnv.obj to make a cnv plot, but get a error. "Error in rep(contig_name, contig_tbl[contig_name]) : invalid 'times' argument". anyone counld help me to fix it? infercnv_all = infercnv::run(infercnv_obj, cutoff=0.1, out_dir= "./infercnv/", cluster_by_groups=T, output_format = "pdf", num_threads=16, denoise=T, HMM=T, no_plot = T)

plot_cnv(infercnv_obj = infercnv_all, out_dir = "./infercnv/", output_filename = "MTumor", output_format = "pdf")

INFO [2023-10-23 11:01:33] ::plot_cnv:Start INFO [2023-10-23 11:01:33] ::plot_cnv:Current data dimensions (r,c)=6635,37599 Total=250323665.284201 Min=0.106880920491228 Max=9.2070584985791. INFO [2023-10-23 11:01:34] ::plot_cnv:Depending on the size of the matrix this may take a moment. INFO [2023-10-23 11:01:46] plot_cnv(): auto thresholding at: (0.825627 , 1.181222) Error in rep(contig_name, contig_tbl[contig_name]) : invalid 'times' argument

Thanks in advance!!

GeorgescuC commented 9 months ago

Hi @lvliang418 ,

What version of infercnv are you running? Could you also post the log of the run that produced that object?

The error seems to be related to the names of the contigs that are listed in infercnv_obj@gene_order[["chr"]]. If you inspect them, can you run table() and unique() on them? Do all names appear valid and non-empty?

Regards, Christophe.