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jeffersonfparil / compare_genomes

A comparative genomics workflow using Nextflow, conda, Julia and R
GNU General Public License v3.0
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Can't generate venn diagram with R script #16

Open jacquelinemattos opened 5 months ago

jacquelinemattos commented 5 months ago

Hi,

All the intermediate files have been created, but I'm still getting an R error to generate the venn diagram:

`Attaching package: VennDiagram The following object is masked from package:ape:

rotate

Error in x[[i]] : index out of bounds Calls: venn.diagram -> unique`

Any suggestions? Thanks so much!!!

jacquelinemattos commented 5 months ago

And this is what it's on my "VennDiagram.2024-04-06_07-18-31.log"

INFO [2024-04-06 07:18:32] [[1]] INFO [2024-04-06 07:18:32] Y[idx] INFO [2024-04-06 07:18:32] INFO [2024-04-06 07:18:32] $col INFO [2024-04-06 07:18:32] colours[idx] INFO [2024-04-06 07:18:32] INFO [2024-04-06 07:18:32] $fill INFO [2024-04-06 07:18:32] colours[idx] INFO [2024-04-06 07:18:32] INFO [2024-04-06 07:18:32] $alpha INFO [2024-04-06 07:18:32] [1] 0.3 INFO [2024-04-06 07:18:32] INFO [2024-04-06 07:18:32] $filename INFO [2024-04-06 07:18:32] NULL INFO [2024-04-06 07:18:32]

jeffersonfparil commented 5 months ago

How many species do you have on your: config/venn_species_max_5.txt?

jacquelinemattos commented 5 months ago

Just four species

jeffersonfparil commented 5 months ago

I'm assuming you have unique species, if that's the case then you may have the same set of genes in both species. I'll try to accommodate for that in the next update.

jacquelinemattos commented 5 months ago

For sure, I'll try removing one of them in my next run. Although I think that my four species are not very closely related among each other. Even the two that would be the most, are not too much. But of course, I'll give this a try, and let you know how it went. Thanks so much!