pathview: unable to use option "out.suffix"
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文祥 • 0
@55f3e2a2
Last seen 4 weeks ago
Japan

Hi

I'm a light user of R, and faced the problem with package "pathview". I tried to use the option "out.suffix", but it didn't work. Output results were over-written due to this problem. This is trouble.


#Here is my code
pathview(gene.data = sample.fc, pathway.id = keggids, species = "hsa", out.suffiX = "sample_name")

# result
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /Users/sakurafumiaki/Desktop/DEseq2
Info: Writing image file hsa04060.pathview.png
Info: Downloading xml files for hsa04061, 1/1 pathways..
Info: Downloading png files for hsa04061, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /Users/sakurafumiaki/Desktop/DEseq2
Info: Writing image file hsa04061.pathview.png
Info: Downloading xml files for hsa04657, 1/1 pathways..
Info: Downloading png files for hsa04657, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /Users/sakurafumiaki/Desktop/DEseq2
Info: Writing image file hsa04657.pathview.png
Info: Downloading xml files for hsa04668, 1/1 pathways..
Info: Downloading png files for hsa04668, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /Users/sakurafumiaki/Desktop/DEseq2
Info: Writing image file hsa04668.pathview.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /Users/sakurafumiaki/Desktop/DEseq2
Info: Writing image file hsa04640.pathview.png

And my environment

OS: macOS BigSur v11.4

Rstudio: version 1.4.1103

pathview : verson 1.32.0

Could anyone can help?

Thank you for your attention

Fumiaki

pathview • 142 views
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R version 4.1.0 (2021-05-18)

Platform: x86_64-apple-darwin17.0 (64-bit)

Running under: macOS Big Sur 10.16

Best Fumiaki

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Hi

I made a mistake. That was a typo! No space was needed after the "out.suffix".

pathview(gene.data = sample.fc, pathway.id = keggids, species = "hsa", out.suffiX="sample_name")

command above was worked. I'm sorry for bother you.

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Entering edit mode
Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 29 days ago
United States

Just a reminder: The typo was not the space, it is the upper case X in out.suffiX. the argument is out.suffix instead, as shown in the subject line.

#your code  
pathview(gene.data = sample.fc, pathway.id = keggids, species = "hsa", out.suffiX = "sample_name")
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