`mcell_mc_split_filt` followed by `mcell_mc2d_force_knn` : length mismatch errror about metacell HOT 5 CLOSED

please paste the output of length(mc@colors) and max(mc@mc), assuming your metacell object is named 'mc'. Assuming this is the mismatch, we'll look into why this mismatch happens when running mcell_mc_split_filt.

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Hi, thanks for the quick response! Indeed this was the mismatch. The output length(mc@colors) was 1, and max(mc@mc) was 22. When I populated mc@colors with 22 colors (e.g. using mc_colorize_default it worked.

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We'll still look into why the length of mc@colors was 1 when running the split function, assuming you didn't set this on purpose. For now coloring in some manner is the workaround

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We did not set anything regarding the colours. If you need a reproducible example, I can email you a subset of data and the code we are using.

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Hi, thanks for the quick response! Indeed this was the mismatch. The output length(mc@colors) was 1, and max(mc@mc) was 22. When I populated mc@colors with 22 colors (e.g. using mc_colorize_default it worked.

Indeed, I have met the similar error as above. After checking mc_outliers.r, here may be the issue:

mcell_mc_split_filt = function(new_mc_id, mc_id, mat_id, T_lfc, plot_mats=T, dirichlet=F)
{
        #......
        new_mc = rep(NA, length(mc@mc))
	names(new_mc) = names(mc@mc)
        #......	
        new_mc = new_mc[setdiff(names(new_mc),new_outliers)]
	scdb_add_mc(new_mc_id, tgMCCov(new_mc, new_outliers, mat))
}

Since new_mc@colors was no assigned, what I'll add to after running mcell_mc_split_filt is as followed:

mcell_mc_split_filt(new_mc_id=paste0(id,'_filt'),   
            mc_id=id, 
            mat_id=id,
            T_lfc=3, plot_mats=F)
# restore mc@colors as one unknown bug-> return 1 after function 'mcell_mc_split_filt'
mc_filt = scdb_mc(paste0(id,'_filt'))
mc_filt@colors = rep(NA, max(mc_filt@mc))
names(mc_filt@colors) = 1:max(mc_filt@mc)
scdb_add_mc(paste0(id,'_filt'),mc_filt)

That takes a fair bit of redundancy as it runs after 'mcell_mc_split_filt' but not in it.

Hope that helps.
Best

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