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?
