the parameter keep_significant_only in plot_cpbd.R is not work

[snow55]

Hi, thank you for your beautiful work.

I'm trying to set keep_significant_only = TRUE when runing plot_cpdb function and setting degs_analysis=TRUE in R, but I found that it can not plot the significant L-R pairs.

Here are my codes:

pvals = read.delim(paste0(dir_out, 'degs_analysis_relevant_interactions_result.txt'), check.names = FALSE) tmp = pvals[ grep("^CXC|CCL|CCR|CX3|XCL|XCR",pvals$interacting_pair),c('interacting_pair','Macrophage|DC','DC|Macrophage')] tmp = tmp[tmp$Macrophage|DC==1 | tmp$DC|Macrophage==1,] #print significant L-R pairs print(tmp)

A data.frame: 6 × 3 interacting_pair Macrophage|DC DC|Macrophage

25 CCL3_CCR1 1 1 26 CCL3L1_CCR1 1 1 28 CCL19_CCRL2 0 1 30 CCL20_CCR6 1 0 68 CXCL9_CXCR3 1 0 69 CXCL10_CXCR3 1 0 >plot_cpdb( scdata = sce_obj, cell_type1 = "Macrophage", cell_type2 = "DC", celltype_key = "Tcelltype", means = means, pvals = pvals, keep_significant_only=TRUE, degs_analysis=TRUE, # genes = c('CXCL10') gene_family = "chemokines" ) Error in plot_cpdb(scdata = sce_obj, cell_type1 = "Macrophage", cell_type2 = "DC", : No significant genes found and plotting will not proceed. Traceback: 1. plot_cpdb(scdata = sce_obj, cell_type1 = "Macrophage", cell_type2 = "DC", . celltype_key = "Tcelltype", means = means, pvals = pvals, . keep_significant_only = TRUE, degs_analysis = TRUE, gene_family = "chemokines") 2. stop("No significant genes found and plotting will not proceed.") Besides, I found that the default setting of keep_significant_only is TRUE which is not consistent with the description. #' @param keep_significant_only logical. **Default is FALSE**. Switch to TRUE if you only want to plot the significant hits from cpdb. plot_cpdb <- function(scdata, cell_type1, cell_type2, celltype_key, means, pvals, interaction_scores = NULL, cellsign = NULL, max_size = 8, **keep_significant_only = TRUE,** splitby_key = NULL, gene_family = NULL, custom_gene_family = NULL, genes = NULL, standard_scale = TRUE, cluster_rows = TRUE, col_option = viridis::viridis(50), default_style = TRUE, highlight_col = "red", highlight_size = NULL, max_highlight_size = 2, special_character_regex_pattern = NULL, degs_analysis = FALSE, return_table = FALSE, exclude_interactions = NULL, min_interaction_score = 0, scale_alpha_by_interaction_scores = FALSE, scale_alpha_by_cellsign = FALSE, filter_by_cellsign = FALSE, title = "", ...) I am wondering whether you could check it and fix these questions. Another question is how we can only plot significant L-R pairs with no other noise L-R pairs? Thank you very much!

[zktuong]

thanks @snow55. would you be able to send to me these files so that can do some more testing?

[snow55]

thanks @snow55. would you be able to send to me these files so that can do some more testing?↳

I'm sorry. Since plot_cpdb function need the sce_object which contains large data, maybe I cannot sent you these files. But what I just do is using cpdb_degs_analysis_method.call() function in python script to get the degs_analysis_relevant_interactions_result.txt. I am wondering whether you can give us a degs analysis tutorial in https://zktuong.github.io/ktplots/articles/vignette.html, rather than mentioned it in a sentence. Thank you very much!

[zktuong]

hi sorry for the delay. ok looks like this is an issue with the documentation. does this behaviour still persist at the python version? in that it's not plotting despite degs_analysis=TRUE ?

[zktuong]

ok i found a bug specifically to do with degs_analysis specifically at

https://github.com/zktuong/ktplots/blob/b70d98bafeb5e202415f3c829ac22da94e97983a/R/plot_cpdb.R#L172-L174

it returns an empty table at the moment, which isn't correct. i will try and see what's going wrong

[zktuong]

it's likely because the new cellphonedb outputs don't have the same dimensions as it used to.

[zktuong]

hi @snow55, can you reinstall ktplots and see if the function works for you now? feel free to reopen if it still doesn't work.

[snow55]

hi @snow55, can you reinstall ktplots and see if the function works for you now? feel free to reopen if it still doesn't work.↳

Sorry for late reply. I have reinstalled the ktplots and it works well now. Thank you very much!