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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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Problem with GO-All gene set #15

Closed saulc27 closed 5 years ago

saulc27 commented 5 years ago

Hello Ege,

Let me first say what great tool pathfindr is! Thanks for the development of this package. I am having troubles when using the GO gene sets.

This is my input which works well for the KEGG and Reactome gene sets

RA_output.sh.GO <- run_pathfindR(path.findr.sh, output_dir = "GO-all", gene_sets = "GO-All")

However when I try the GO gene sets I get this errors,

Error in grDevices::png(paste0("pathway_visualizations/", current_row$Pathway, : unable to start png() device brane(4)&integral_component_of_lumenal_side_of_endoplasmic_reticulum_membrane(5) In addition: Warning messages: 1: In pathfindR::input_processing(input, p_val_threshold, pin_path, : pathfindR cannot handle p values < 1e-13 These were changed to 1e-13 2: In grDevices::png(paste0("pathway_visualizations/", current_row$Pathway, : unable to open file 'pathway_visualizations/lumenal_side_of_membrane(3)&lumenal_side_of_endoplasmic_reticulum_membrane(4)&integral_component_of_lumenal_side_of_endoplasmic_reticulum_membrane(5).png' for writing 3: In grDevices::png(paste0("pathway_visualizations/", current_row$Pathway, : opening device failed

No output table/file is created

Thank you, Saul Carcamo

egeulgen commented 5 years ago

hey @saulc27,

the final commit 74b020797c5bfdf4bb5f1847f31a19f74599872a should fix this issue. If not, make sure you have the correct permissions to write files under the current directory. If visualization of pathway diagrams is not essential for you, set visualize_pathways to FALSE. To get the latest dev version of pathfindR:

install.packages("devtools") # if you have not installed "devtools" package
devtools::install_github("egeulgen/pathfindR")
saulc27 commented 5 years ago

Thank you Ege, It's working now!