Closed saulc27 closed 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")
Thank you Ege, It's working now!
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