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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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ERROR about cluster_by_groups=FALSE #478

Open xiasijian opened 1 year ago

xiasijian commented 1 year ago

image

Hello, thank you for your excellent software. I got this error when I set cluster_by_groups=FALSE. Maybe I need to set TRUE, but I do not want to rerun infercnv, because it took a long time to run. How can I draw plot by myself?

GeorgescuC commented 1 year ago

Hi @xiasijian ,

To manually plot a figure, you should first load the latest backup object (change the name in the command) into your R session with infercnv_obj_backup = readRDS("run.final.infercnv_obj"). You can then call plot_cnv() with that object and the combination of settings you prefer.

Because you are getting an error likely related to clustering, which might happen again, you may have to reset the slot infercnv_obj_backup@tumor_subclusters = NULL so that a new hclust is run on the fly while plotting.

Regards, Christophe.