I am trying to use Pathview to visualise some expression data. This is my example data input as test.csv
| id | fc |
|---|---|
| AJAP_14870 | -0.04 |
| AJAP_14875 | 0.32 |
| AJAP_14880 | -0.06 |
| AJAP_14885 | 0.15 |
| AJAP_14890 | -0.52 |
| AJAP_14895 | -0.39 |
| AJAP_14900 | 0.16 |
This code works great to get the KEGG pathway output image, however, it doesnt give the gene expression gradient on the image.
geneList = test[,2]
> names(geneList) = as.character(test[,1])
> geneList = sort(geneList, decreasing = TRUE)
> gene <- names(geneList)[abs(geneList) > 2]
>
> kk <- enrichKEGG(gene = gene,
+ organism = 'aja',
+ pvalueCutoff = 0.05)
> browseKEGG(kk, 'aja01055')
For pathview I am trying
aja01055 <- pathview(gene.data = test,
+ pathway.id = "aja01055",
+ species = "aja",
+ limit = list(gene=max(abs(geneList)), cpd=1))
But get the error:
Note: Mapping via KEGG gene ID (not Entrez) is supported for this species,
it looks like "AJAP_04105"!
Info: Getting gene ID data from KEGG...
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) :
Bad Request (HTTP 400).
Any help would be greatly appreciated!