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wu-yc / scMetabolism

Quantifying metabolism activity at the single-cell resolution
BSD 3-Clause "New" or "Revised" License
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BoxPlot.metabolism issue, obj not in function code #2

Open msalaciak opened 2 years ago

msalaciak commented 2 years ago

I noticed BoxPlot wasn't working, couldn't find countexp.Seurat

Turns out in the function, the Countexp.Seurat was not replaced by parameter = obj

https://github.com/wu-yc/scMetabolism/blob/9b79b07483bcf229d12aef4356873716e488fcfe/R/visualize_metabolism.R#L174-L180

wu-yc commented 2 years ago

Hi Salaciak,

Thanks for your comment. We are now working on it and will revise the code ASAP

xutongran commented 2 years ago

Hi Wu yc ! I had a similar problem, when i run this command "DotPlot.metabolism(obj = countexp.Seurat, pathway = input.pathway, phenotype = "ident", norm = "y")", Error in [.data.frame(metadata, , input.parameter) : 选择了未定义的列, I want to request you: how to fix this kind of error

kake1998 commented 2 years ago

Why can't you install this package?

sergio-rutella commented 1 year ago

The boxplot issue has not been resolved yet. I am working with this package now and I keep getting the same error!

msalaciak commented 1 year ago

@sergio-rutella What I did to fix it is I just copied the entire function from here and just changed all instances of Seurat to the parameter obj and it works!

https://github.com/wu-yc/scMetabolism/blob/9b79b07483bcf229d12aef4356873716e488fcfe/R/visualize_metabolism.R#L174-L210