Problems plotting interactions with multiple words in cpdb4

[jweefergs]

Hi,

Thank you for this very helpful package - I'm having a lot of fun plotting my data!

However, I'm having trouble plotting specific interactions which include multiple words (such as IL18-IL18-receptor) in plot_cpdb4. The below should be a significant interaction, as is plotted as such in plot_cpdb, and I can plot other interactions (such as CXCL2-DPP4) without problem in plot_cpdb4. Can you advise?

plot_cpdb4( = sce,
interaction = "IL18-IL18_receptor", #IL18_IL18_receptor also tried
cell_type1 = "CD56posCD16neg_NK",
cell_type2 = "Mast_cells",
celltype_key = "cell_annotation",
means = means,
pvals = pvals,
deconvoluted = decons,
degs_analysis = TRUE
)

I get the following error:
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 't': 'data' must be of a vector type, was 'NULL'

From the looks of things, it is struggling to handle the "-" in the first string splitting step. Also, in the input data for parameter means and pvals, gene_b value was blank for those that did not work and filled for those that did (example attached). Is this indicative of an issue upstream as well?

Many thanks!
means_example.csv

[zktuong]

hi @jweefergs! Thank you for your interest and for bringing this up to me.

I found the issue but i will need time to implement a fix.

For now, can you try specifying the interaction as "IL18 receptor-IL18"

The bug is here:

ktplots/R/plot_cpdb4.R

Lines 44 to 56 in a7bb0e6

	genes <- strsplit(interaction, "-")
	genesx <- unlist(lapply(genes, function(g) {
	c(paste(g, collapse = "-"), paste(rev(g), collapse = "-"))
	}))
	if (class(scdata) == "Seurat") {
	stop("Sorry not supported. Please use a SingleCellExperiment object.")
	}
	lr_interactions <- plot_cpdb(scdata = scdata, cell_type1 = ".", cell_type2 = ".",
	celltype_key = celltype_key, splitby_key = splitby_key, means = means, pvals = pvals,
	keep_significant_only = keep_significant_only, standard_scale = standard_scale,
	return_table = TRUE, degs_analysis = degs_analysis, ...)
	lr_interactions <- lr_interactions[gsub(paste0(".*", SPECIAL_SEP), "", lr_interactions$Var1) %in%
	genesx, ]

basically, i ran the last line but with a grep and this is what it returns:

grep("IL18", gsub(paste0(".*", SPECIAL_SEP), "", lr_interactions$Var1), value=TRUE)
  [1] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
  [4] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
  [7] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [10] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [13] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [16] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [19] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [22] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [25] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [28] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [31] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [34] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [37] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [40] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [43] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [46] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [49] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [52] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [55] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [58] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [61] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [64] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [67] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [70] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [73] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [76] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [79] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [82] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [85] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [88] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [91] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [94] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
 [97] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[100] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[103] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[106] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[109] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[112] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[115] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[118] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[121] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[124] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[127] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[130] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[133] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[136] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[139] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"
[142] "IL18 receptor-IL18" "IL18 receptor-IL18" "IL18 receptor-IL18"

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.