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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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Error of computing tumor subclusters via leiden #473

Open hahia opened 1 year ago

hahia commented 1 year ago

Hello, I want to use infercnv to define subclone, but there was a problem image

GeorgescuC commented 1 year ago

Hi @hahia ,

This is an issue with the Leiden package that calls to a Python implementation that we have now dropped. The version of infercnv that is available on the master branch of github fixes the issue by using igraph instead, so you can install that one instead. Alternatively, the new Bioconductor release that is scheduled for next week will bring the fix to the stable release there as well.

Regards, Christophe.

hahia commented 1 year ago

Hi @hahia ,

This is an issue with the Leiden package that calls to a Python implementation that we have now dropped. The version of infercnv that is available on the master branch of github fixes the issue by using igraph instead, so you can install that one instead. Alternatively, the new Bioconductor release that is scheduled for next week will bring the fix to the stable release there as well.

Regards, Christophe.

OK!! thank you for your reply

hahia commented 1 year ago

Hi @hahia ,

This is an issue with the Leiden package that calls to a Python implementation that we have now dropped. The version of infercnv that is available on the master branch of github fixes the issue by using igraph instead, so you can install that one instead. Alternatively, the new Bioconductor release that is scheduled for next week will bring the fix to the stable release there as well.

Regards, Christophe.

Hi, I update the infercnv by devtools::install_github("broadinstitute/infercnv"). But there are no infercnv.reference.txt and infercnv.observations.txt.

GeorgescuC commented 1 year ago

Hi @hahia ,

Those files are generated at the same type as the plots if the "write_expr_matrix" option is set to TRUE, but the default is now set to FALSE and properly linked with plot_cnv. If you simply restart the same run of infercnv you already did but changing this option, it should reload a backup from the end of the process and simply plot the figure again while this time outputting the files.

Regards, Christophe.