Error in h(simpleError(msg, call))

[AShahzad9]

Hi,

I have been trying to use the plot_cpdb2 function to create the chord plots but I keep getting this error:

**> p <- plot_cpdb2(cell_type1 = 'fibroblast', cell_type2 = 'monocytes',

• scdata = merged_obj.sce,
• idents = 'label', # column name where the cell ids are located in the metadata
• means = out_mean,
• pvals = out_pvalues,
• deconvoluted = out_deconvoluted, # new options from here on specific to plot_cpdb2
• desiredInteractions = list(
• c('monocytes', 'fibroblast'),
• c('fibroblast', 'monocytes')),
• interaction_grouping = interaction_annotation,
• edge_group_colors = c(
• "Activating" = "#e15759"
• ),
• node_group_colors = c(
• "monocytes" = "red",
• "fibroblast" = "blue"),
• keep_significant_only = TRUE,
• standard_scale = TRUE,
• remove_self = TRUE
• ) Error in h(simpleError(msg, call)) : error in evaluating the argument 'i' in selecting a method for function '[': error in evaluating the argument 'x' in selecting a method for function 'which': subscript contains invalid names]**

Can you help me understand this better and help me fix it?

Thanks, A

[zktuong]

Hi, can you post the full error log for me? just want to see which line number this error is appearing on.

Are there any weird characters in your label column? like +, / etc.

[AShahzad9]

Hi ,

"Error in h(simpleError(msg, call)) : error in evaluating the argument 'i' in selecting a method for function '[': error in evaluating the argument 'x' in selecting a method for function 'which': subscript contains invalid names"

Is that what you were after- have also attached a screenshot.

Does Cpdb2 not work with seurat files ?

There are only underscores in the column, I think

[zktuong]

Yea it only works with SingleCellExperiment object. Just convert with Seurat’s as.SingleCellExperiment

I’m not sure what else could be triggering this

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