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ELTEbioinformatics / mulea

mulea - an R package for enrichment analysis using various ontologies and empirical false discovery rate
https://www.biorxiv.org/content/10.1101/2024.02.28.582444v1
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Error when plot_lollipop with the reshaped gsea results #8

Closed barizona closed 9 months ago

barizona commented 9 months ago

There is a segmentation error when plotting lollipop with the gsea reshaped results: "Quitting from lines 480-487 [lollipop_plot_gsea] (README.Rmd) Error in geom_segment(): ! Problem while computing aesthetics. ℹ Error occurred in the 1st layer. Caused by error: ! object 'eFDR' not found Backtrace:

  1. rmarkdown::render(...)
  2. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  3. knitr:::process_file(text, output)
  4. knitr:::process_group.block(group)
  5. knitr:::call_block(x) ...
    1. ggplot2 (local) f(l = layers[[i]], d = data[[i]])
    2. l$compute_aesthetics(d, plot)
    3. ggplot2 (local) compute_aesthetics(..., self = self)
    4. base::lapply(aesthetics, eval_tidy, data = data, env = env)
    5. rlang (local) FUN(X[[i]], ...) Execution halted"

Therefore in the README I set it to eval=FALSE till correcting this error. @olbeimarton , can you correct it? Or @koralgooll ?

olbeimarton commented 9 months ago

Hi, I'm not getting this error. However, since updating the column names to snake case the axis and legend titles are: get(ontology_id_colname) and get(p_value_type_colname). @koralgooll can you please check this? I only replaced the name in SubramanianTest.R (see commit: https://github.com/ELTEbioinformatics/mulea/commit/2da673259fc68a97b36becce855182de38811f9c). I can manually rename them if you'd like with the ggplot xlab, ylab and labs functions.

barizona commented 9 months ago

Yes, now it runs for me as well. Maybe it was an RStudio error (sometimes when I restart RStudio some errors disappear)? Now the plot looks like this: image

barizona commented 9 months ago

I have corrected the function