i used the output of enrichKEGG function from the package clusterProfiler, in order to visualize a resulted enriched KEGG pathway, via the R package pathview:
i used the following code, where genes_change is a vector of log fold changes with names as the EntezGene IDs:
> hsa03030 <- pathview(gene.data = genes_change,pathway.id = "hsa03030", species="hsa",kegg.native=F,limit= list(gene=max(abs(genes_change)), cpd=1), sign.pos="bottomleft",keys.align = "y")
But then, i got the following message:
Info: Downloading xml files for hsa03030, 1/1 pathways..
Info: Downloading png files for hsa03030, 1/1 pathways..
Note: hsa03030 not rendered, 0 or 1 connected nodes!
Try "kegg.native=T" instead!
In download.file(xml.url, xml.target, quiet = T) :
downloaded length 18415 != reported length 200
Naively speaking, this means that for graphviz output, my DE genes on the specific pathway(26 DE genes found on this pathway) are somehow "isolated" and dont have sufficient interactions ? Or the "Note" output has a different meaning ?? Maybe this is happening because this specific pathway is the DNA replication ??