I have problems with GOchord function in GOplot (https://wencke.github.io/). When I load data with ensembleID (ENSRNOG00000000007) it works fine, but when I load data with Gene Symbols (Gad1) it gives me only the first gene in chord and couldnot build the matrix. May be I should load some more libraries?
With gene Symbols:
head(chord) immune response RT1-CE10 1 peptide antigen assembly with MHC class II protein complex RT1-CE10 0 regulation of protein phosphorylation response to bacterium RT1-CE10 0 0 response to hypoxia logFC RT1-CE10 0 0.842166
With EnsembleID:
head(chord) immune response ENSRNOG00000000451 1 ENSRNOG00000001480 0 ENSRNOG00000003807 0 ENSRNOG00000003869 0 ENSRNOG00000004077 0 ENSRNOG00000004089 1 peptide antigen assembly with MHC class II protein complex ENSRNOG00000000451 0 ENSRNOG00000001480 0 ENSRNOG00000003807 0 ENSRNOG00000003869 0 ENSRNOG00000004077 0 ENSRNOG00000004089 0 regulation of protein phosphorylation ENSRNOG00000000451 0 ENSRNOG00000001480 0 ENSRNOG00000003807 1 ENSRNOG00000003869 0 ENSRNOG00000004077 0 ENSRNOG00000004089 0 response to bacterium response to hypoxia ENSRNOG00000000451 0 0 ENSRNOG00000001480 1 0 ENSRNOG00000003807 0 0 ENSRNOG00000003869 0 1 ENSRNOG00000004077 0 0 ENSRNOG00000004089 0 0 action potential logFC ENSRNOG00000000451 0 5.602350 ENSRNOG00000001480 0 1.838350 ENSRNOG00000003807 0 1.439280 ENSRNOG00000003869 0 -0.545484 ENSRNOG00000004077 1 0.758108 ENSRNOG00000004089 0 -1.050340
GObar, GOBubble and GOcicrcle works fine on files with Gene Symbols. How ensembleID's could be converted in symbols on GOChord graphs, if there is no other solution?
