Question

only 0's may be mixed with negative subscripts

2

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nature.hunger ▴ 30

@naturehunger-10178

Last seen 7.9 years ago

I got an Error about only 0's may be mixed with negative subscripts. I read a txt file as data.frame , it has more than 100 rows with 2 columns. And 4 genes are enriched in hsa04215 pathway. And I extract it from data.frame and transform to a vector, look like
> xx
      836       596      5599     10018 
-7.755529 -3.458985 -2.453181 -1.870450 
> hsa04215 <- pathview(gene.data=xx,
+                      pathway.id="hsa04215",
+                      species ="hsa")
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory D:/desktop_folder
Info: Writing image file hsa04215.pathview.png
Info: some node width is different from others, and hence adjusted!
Error in img[pidx[i, 3]:pidx[i, 4], sel.px, 1:3] :
  only 0's may be mixed with negative subscripts

pathview • 3.5k views

ADD COMMENT • link updated 20 months ago by saadatabu1996 ▴ 10 • written 7.9 years ago by nature.hunger ▴ 30

score 1 · Answer 1 · 2017-01-04

1

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nature.hunger ▴ 30

@naturehunger-10178

Last seen 7.9 years ago

These days I got an answer from your Pathview web server. Because it has no hsa04215 pathway in your web server. But it has hsa04215 pathway in KEGG website (http://www.kegg.jp/pathway/hsa04215).

ADD COMMENT • link 7.9 years ago nature.hunger ▴ 30

score 1 · Answer 2 · 2023-02-28

1

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saadatabu1996 ▴ 10

@52e2d9db

Last seen 20 months ago

Italy

In pathview KEGG visualization, setting "same.layer" to FALSE fixed the problem for me.

ADD COMMENT • link 20 months ago saadatabu1996 ▴ 10

score 0 · Answer 3 · 2017-10-30

0

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map2085 ▴ 40

@map2085-9227

Last seen 6.6 years ago

United States

I have same problem

ADD COMMENT • link 7.0 years ago map2085 ▴ 40