pathfindR
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egeulgen
Duplicated factor level when creating term_gene_heatmap
Hello, I'm getting this bug when attempting to make the term_gene_heatmap for GO_BP results. Execution is halted here for GO_BP but not for the other pathways that I've been able to run so far (GO_MF and GO_CC). I checked the clustered term file and found a duplicate entry. Could this be causing the issue? One GO term is listed as a member for two clusters? I'm not sure what would be causing this issue.
Error in levels<-(*tmp*, value = as.character(levels)) :
factor level [8] is duplicated
Calls: pathfindR_enrichment -> run_pathf -> print -> term_gene_heatmap -> factor
Execution halted
Desktop (please complete the following information):
- OS: Rhel8
- Version 1.6.3
Hello,
Would you mind sharing the data frame as an RDS file so I can try to reproduce the issue?
Hello,
Would you mind sharing the data frame as an RDS file so I can try to reproduce the issue?
I'm trying to upload the file in the comment but I'm getting a warning saying that the file type isn't supported
This also occurs sometimes for the output of other pathways. For example, when re-running pathfindR, GO_BP didn't produce this error, but Reactome did. This is on the same dataset with the same parameters (n_iter = 10, min g_set = 10, max g_set = 300)
[1] "enrichment_Reactome"
Number of genes provided in input: 9027
Number of genes in input after p-value filtering: 104
Could not find any interactions for 2 (1.92%) genes in the PIN
Final number of genes in input: 102
Found 86 active subnetworks
Found 195 active subnetworks
Found 195 active subnetworks
Found 158 active subnetworks
.
.
Number of genes provided in input: 9027
Number of genes in input after p-value filtering: 104
Could not find any interactions for 2 (1.92%) genes in the PIN
Final number of genes in input: 102
Number of genes provided in input: 9027
Number of genes in input after p-value filtering: 104
Could not find any interactions for 2 (1.92%) genes in the PIN
Final number of genes in input: 102
Error in `levels<-`(`*tmp*`, value = as.character(levels)) :
factor level [9] is duplicated
Calls: pathfindR_enrichment -> run_pathf -> print -> term_gene_heatmap -> factor
pdf(file = paste0("term_gene_heatmap_", enrichment_db, ".pdf"), width = 11.69, height = 8.27)
print(term_gene_heatmap(result_df = output_df_pathfindR, genes_df = input_df_pathfindR, use_description = TRUE,
num_terms = 10))
dev.off()
can you zip together the RDS files for output_df_pathfindR and input_df_pathfindR and share it? The zip should be allowed to be uploaded
I cannot reproduce this issue. Can you try downloading the latest development version and see if this resolves the issue?
install.packages("devtools") # if you have not installed "devtools"
devtools::install_github("egeulgen/pathfindR")
Sorry, I may have attached one that passed on a different pathway. Here is a zip folder with input/output dateframes. In this example, the error occurs when printing the term gene heatmap for the cell markers pathway. Here is the error: New Folder With Items.zip
Final number of genes in input: 102
Error in `levels<-`(`*tmp*`, value = as.character(levels)) :
factor level [7] is duplicated
Calls: pathfindR_enrichment -> run_pathf -> print -> term_gene_heatmap -> factor
In the meantime, I'll install the dev version locally and test again This may take a lot more time though because my local workstation is very slow.
Hello again, I couldn't reproduce the issue with this data either. Please try the latest development version and let me know if it persists
Really strange. I am not able to replicate the errors locally either but these appear on our server for multiple members of our team. Could this be a package issue? I've attached the results from session_info() below.
Also, I checked the version that we are using in our server and it is up to date with the latest pathfindR version 1.6.4.
Session info ---------------------------------------------------------------
setting value
version R version 4.1.2 (2021-11-01)
os CentOS Linux 7 (Core)
system x86_64, linux-gnu
ui X11
language (EN)
collate C
ctype C
tz America/New_York
date 2022-09-07
pandoc 2.11.2 @ /programs/x86_64-linux/system/biogrids_bin/pandoc
- Packages -------------------------------------------------------------------
package * version date (UTC) lib source
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can you debug by running term_gene_heatmap() after running debugonce(term_gene_heatmap) and tell me on which line the error occurs? This might help us pinpoint the issue