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gogadget use with non-model organism to visualize goseq results

I am trying to use gogadget visualize the results from my goseq analysis. I seem to be able to correctly obtain the adjusted p values from gogadget.p.adjust, and gogadget.explore to pick a range to filter my results. My issue is in using the gogadget.heatmap function:

gogadget.heatmap(GO.filtered, geneNames, gene2cat = geneID32GO)

where GO.filtered = my filtered go.p.adj object geneNames = vector of all assayed genes gene2cat = my GO category mappings used in place of organism and genome in goseq function

I get this error:

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'stack': error in evaluating the argument 'x' in selecting a method for function 'match': argument "genome" is missing, with no default

The genome is missing on purpose, as this is a non model organism, and I tried to just put in the GO category mappings used for my goseq object.

Has anyone been able to work around missing a genome for use in this function, like we are able to in the goseq package? Or can anyone suggest a graphical interface to use with goseq or topgo results witha. nonmodel organism?

gogadget go enrichment go goseq rna-seq
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written by arroyo.sr • arroyo.sr

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