GOplot error - Gene Ontology plot generation errors
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2.1 years ago
Light92 ▴ 60

Hello, I'm trying to run the Trinity script prepnrunGOplot.pl to get plots after GO enrichment analysis (calculated with analyzediff_expr.pl), comparing two samples previously DE analyzed. It calls the goplot package, but I'm getting errors I can't understand

I ran:

./prep_n_run_GOplot.pl --GO_annots /home/genomica/DATA/Lattuga/go_annots.dat --DE_subset /home/genomica/DATA/Lattuga/edgeR_0.2/Matrici.gene.counts.matrix.DRR057333_48h_vs_DRR057083_48h.edgeR.DE_results.P0.001_C2.DE.subset --DE_GO_enriched /home/genomica/DATA/Lattuga/edgeR_0.2/Matrici.gene.counts.matrix.DRR057333_48h_vs_DRR057083_48h.edgeR.DE_results.P0.001_C2.DE.subset.GOseq.enriched --tmpdir /home/genomica/DATA/Lattuga/GOPLOT --pdf_filename GOPLOT_48LL_VS_48LD

And got this:

WARNING, no GO term info found for: GO:0044763, skipping...
    WARNING, no GO term info found for: GO:0044710, skipping...
    WARNING, no GO term info found for: GO:0051183, skipping...
    WARNING, no GO term info found for: GO:0044711, skipping...
    CMD: /mnt/d8e73111-db5e-4011-87aa-e4d64fb8c1e9/DATA/Software/Trinity/trinityrnaseq-2.8.5/Analysis/DifferentialExpression/GOplot.Rscript --EC_david /home/genomica/DATA/Lattuga/GOPLOT/EC.david --EC_genelist /home/genomica/DATA/Lattuga/GOPLOT/EC.genelist --pdf_outfile GOPLOT_48LL_VS_48LD
    Carico il pacchetto richiesto: ggplot2
    Carico il pacchetto richiesto: ggdendro
    Carico il pacchetto richiesto: gridExtra
    Carico il pacchetto richiesto: RColorBrewer
    Generating plot pdf file: GOPLOT_48LL_VS_48LD
    GOBar, circ, BP
    GOBar, circ, multiple
    GOBar, multiple, Z-scores
    GOBubble, multiple
    Warning message:
    Removed 115 rows containing missing values (geom_point).
    GOBubble, bckgrd color
    Warning message:
    Removed 115 rows containing missing values (geom_point).
    GOCircle
    Error in f(..., self = self) : Breaks and labels are different lengths
    Calls: GOCircle ... guide_train -> guide_train.colorbar -> <Anonymous> -> f
    Inoltre: Warning messages:
    1: Removed 5 rows containing missing values (geom_point).
    2: Removed 5 rows containing missing values (geom_point).
    Esecuzione interrotta
    Error, CMD: /mnt/d8e73111-db5e-4011-87aa-e4d64fb8c1e9/DATA/Software/Trinity/trinityrnaseq-2

Can anyone help me here? Thanks in advance. What could be wrong in my input files?

If need I can attach them.

goplot gene ontology trinity bioconductor • 698 views
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I would assume that something is wrong with the input files (sorry, somehow unspecific :)

I would compare your input data with exemplary input files (I hope the creators of this tool provided them).

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