error with single cell summary object about conos HOT 5 CLOSED

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@pkharchenko , you missed the required part with creating Pagoda or Seurat objects. So it should be something like lapply(sceList, counts) %>% lapply(basicSeuratProc) %>% Conos$new()

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Thanks a lot for all of your suggestions.
i tried

sce1_counts=counts(sce1)
counts=lapply(sceList, counts)
panel.preprocessed <- lapply(counts, basicP2proc, n.cores=4, min.cells.per.gene=0, n.odgenes=2e3, get.largevis=FALSE, make.geneknn=FALSE)

is this simmilar to lapply(sceList, counts) %>% lapply(basicSeuratProc) %>% Conos$new() ?
I am not sure if the next question should be a separate thread.
how to add annotation(label) for cells for their distinct cell type? how to integrate that information using conos. I have seen Conos adding labels. I am not sure how to do that for my dataset.
Thanks

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@bony45 The piece of code you supplied will only get you a list of pagoda2 objects. If you want a cobos object you still need to run conos$new(panel.preprocessed).

Regarding your second question(s), that depends on what exactly you want to do. Have you already run the cell clustering and have the desired annotation in a factor ordered according to cell names?
Then you can just do:

con$clusters$your_annotation$groups <- labels

If you don't have the clustering yet, do it with conos and then replace the default labels (numbers) with the ones you want:

con <- Conos$new()
con$findCommunities(method=leiden.community)
labels <- con$clusters$leiden$groups
labels <- revalue(labels, c("1"="your_label1", "2"="your_label2", ...))
con$clusters$your_annotation$groups <- labels

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Thanks a lot

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