Dear Community,
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!
Warning message:
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 ??
Dear Luo, thank you for your explanation !! Maybe i could also naively assume that due to the "complex nature" of this pathway, i have the above warning, because the number of 26 DE genes annotated in this KEGG pathway is not so small. On the other hand, i tried Graphviz output, because it shows more information about the interactions among the nodes and the signalling propagation.
Best,
Efstathios
Dear Luo,
please excuse me for posting again---based on your suggestion, i tried also the native KEGG graph, and i had two further quick questions for the interpretation of the graph:
1) If i use hsa04110 <- pathview(gene.data = lfcs,pathway.id = "hsa04110",
species = "hsa",limit = list(gene=max(abs(lfcs)), cpd=1), same.layer=F)
When i use the argument same.layer=F with the native kegg view, then the original KEGG gene labels are replaced by original gene symbols, correct ?
2) Secondly, i saw for instance from the above resulted graph, that some individual genes are presented more than 1 time in the graph--thus naively that means that these specific genes could participate to more than one specific interaction and/or association in the specific path ?
Thank you for your consideration on this matter !!