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Question: Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
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gravatar for svlachavas
2.0 years ago by
svlachavas570
Greece/Athens/National Hellenic Research Foundation
svlachavas570 wrote:

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 ??

 

 

ADD COMMENTlink modified 2.0 years ago by Luo Weijun1.4k • written 2.0 years ago by svlachavas570
2
gravatar for Luo Weijun
2.0 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
This means that for this particular pathway, there is no interaction between nodes based on data parse from XML file. Hence no real pathway/network can be rendered by Graphviz view. It is recommended to visualize your data using native KEGG graph (which has a prettier layout in such case). For details on this pathway: http://www.genome.jp/kegg-bin/show_pathway?hsa03030
ADD COMMENTlink written 2.0 years ago by Luo Weijun1.4k

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

 

ADD REPLYlink written 2.0 years ago by svlachavas570

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 !!

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by svlachavas570
1
gravatar for Luo Weijun
2.0 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
The answer is true to both your questions. For question 1, you can find more info on same.layer = F on page 5 (for native kegg view) and page 8 (for graphviz view) in pathview vignette or tutorial. For question 2, a node can include 1 or multiple genes with similar function. A gene node may participate in more than 1 interaction/function in 1 or more pathways.
ADD COMMENTlink written 2.0 years ago by Luo Weijun1.4k

Dear Luo,

thank you again for your verification !!

ADD REPLYlink written 2.0 years ago by svlachavas570
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