Error in h(simpleError(msg, call)): While computing the parameter "x" for the function "t", an error occurred: 'data' must be a vector, but it is 'NULL' now In plot4

[wuxiangning]

I encountered this issue mentioned by someone before, and it seems that this problem has not been resolved. Whether I use _, -, or spaces to adjust my interaction pairs, I always get this error. Why is this happening? I used debug to find the bug,it shows like below. debug(plot_cpdb4) plot_cpdb4( interaction=c('IL18 receptor-IL18'),#新的参数 cell_type1='Neu_02_CCL4',cell_type2='Neu_03_IFIT1', scdata=sce_obj, celltype_key="celltype",

idents='celltype',

means=means, pvals=pvals, deconvoluted=deconvoluted2, keep_significant_only=TRUE, standard_scale=TRUE, ) Help!Thanks.

[zktuong]

does this interaction come up as significant with plot_cpdb?

[wuxiangning]

Of course, because I want to select and only look at the proportion of specific interaction pairs, or I want to see the proportion of certain cell types in the total number of interactions.

[zktuong]

I think, curently the error message is essentially complaining that this interaction is not being found, returning an empty table and hence NULL.

hmm, ok. can you send your cellphonedb result files and your singlecellexperiment/seurat object to me at z.tuong@uq.edu.au and i can try and see if i can diagnose what's the issue?

[wuxiangning]

I have sent my data, please check. Much appreciated.

[zktuong]

hi, is your code chunk correct for the data you sent me?

plot_cpdb4(
interaction=c('IL18 receptor-IL18'),#新的参数
cell_type1='Neu_02_CCL4',cell_type2='Neu_03_IFIT1',
scdata=sce_obj,
celltype_key="celltype",
#idents='celltype',
means=means,
pvals=pvals,
deconvoluted=deconvoluted2,
keep_significant_only=TRUE,
standard_scale=TRUE,
)

I ask that because there's no Neu_02_CCL4 or Neu_03_IFIT1 in what you sent.

all i see in the available celltypes are:

the annotations in your your test_cellphonedb.tsv metadata also doesn't seem to match.

[zktuong]

closing for now as more information is needed.