proble Please check your options for splitby_key and your celltypes.

[dd123456000]

I encountered the following issue while using plotcb.

I've tried changing many things, but I'm still getting the same error.

[dd123456000]

[dd123456000]

[dd123456000]

"I changed 'celltype' to 'cell_type,' and now I'm encountering the error 'Error in c_type1[[i]]: subscript out of bounds.'"

[zktuong]

Does the "celltype" or "cell_type" exist in your seurat@meta.data? Also remove the the split.by argument - don't provide NA to it.

[luostrowski]

I'm having the same problem. The "predicted" column exists in the object (ad is a SingleCellExperiment object).

plot_cpdb2(
    scdata = ad,
    cell_type1 = "HSC",
    cell_type2 = ".",
    celltype_key = "predicted", # column name where the cell ids are located in the metadata
    means = means,
    pvals = pvals,
    deconvoluted = HD_deconv 
)

Error in plot_cpdb(scdata = scdata, cell_type1 = cell_type1, cell_type2 = cell_type2, : Please check your options for splitby_key and your celltypes.

[zktuong]

hi @luostrowski, just in case, can you check if the means and pvals are the correct ones that match to your ad object. when library(ktplots) is called, it will also load the internal data (also called means and pvals). this may overwrite your actual objects.

[luostrowski]

Hi! Thank you for the prompt reply! I changed the names of the data frames to make sure it was not being overwritten, but I got the same error :(

plot_cpdb2(
    scdata = ad,
    cell_type1 = "HSC",
    cell_type2 = ".",
    celltype_key = "predicted", # column name where the cell ids are located in the metadata
    means = HD_means,
    pvals = HD_pvals,
    deconvoluted = HD_deconv
)

Error in plot_cpdb(scdata = scdata, cell_type1 = cell_type1, cell_type2 = cell_type2, : Please check your options for splitby_key and your celltypes.

[zktuong]

would you be able to share your files (ad, HD_means, HD_pvals, HD_deconv) so that i can do some testing? I just sent you the secure voucher link via filesender (to your gmail)

[zktuong]

issue may be related to https://github.com/zktuong/ktplotspy/issues/51

[zktuong]

seems like the fix introduces further bugs (e.g. plotting non-significant interactions). need to think of a different solution

[stale[bot]]

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