Problem is plotting plot_cpdb4

[stalware]

Hello, I am working on visualizing cellphones results and am interested in generating a figure using plot_cpdb4. However I am getting an issue when I am using my data

I am using the following code plot_cpdb4( interaction = c('VEGFA-KDR','VEGFA-EPHB2','NRP2-VEGFA'), cell_type1 = 'Cluster_12|Cluster_14', cell_type2 = c('Cluster_17|Cluster_5','Cluster_11|Cluster_7'), scdata = sce, celltype_key = 'cell_type', means = means, pvals = pvals, deconvoluted = decon, desiredInteractions = list( c("Cluster_12", "Cluster_17"), c("Cluster_12", "Cluster_5"), c("Cluster_14", "Cluster_7") ), keep_significant_only = TRUE, standard_scale = TRUE, )

I get the following error: Error in c_type1[[i]] : subscript out of bounds Attached below test file for means: Appreciate the help!!

test_means.txt

[zktuong]

Hi! Is it celltype or cell_type?

[stalware]

Hi! it is celltype, just copied the wrong example. Also, there is another error that pops up - Error in plot_cpdb(scdata = scdata, cell_type1 = ".", cell_type2 = ".", : No significant hits.

Is this because it the specific interaction pair is not significant? I have tried using other pairs as well.

[zktuong]

Did you run cellphonedb in deg_analysis mode? If so, you would need to add deg_analysis=TRUE for every function.

[zktuong]

But yea - you can also toggle the keep significant only option so then it should try to plot everything

[stalware]

cellphondb was run with statistical_analysis. Also tossing off the keep_significant_only option also does not seem to work.

[zktuong]

Hmm ok. Could you send me your cellphonedb output files and the sce object (without gene expression is fine) so i can do more testing after the holidays? z.tuong@uq.edu.au

[zktuong]

closing this for now as the issue seems to be that the DefaultAssay in the seurat object was integrated instead of RNA, so those genes weren't in the single-cell object