Visualization error

[andrisvAria]

Hi,
I am trying to visualize cnv calls from example1 of PennCNV but I have two problems. First, when I run visualize_cnv.pl -format plot -signal offspring.txt ex1.rawcnv I get this output

NOTICE: Signal values for 4 CNV regions are found in offspring.txt
NOTICE: Processing sample offspring.txt CNV chr11:55603545-55669650 with copy number of 0 ... written to offspring.txt.chr11.55603545.PDF
NOTICE: Processing sample offspring.txt CNV chr11:81792950-81806219 with copy number of 1 ... Use of uninitialized value in numeric gt (>) at C:\Users\andsav\Desktop\PennCNV-1.0.5\PennCNV-1.0.5\visualize_cnv.pl line 204.
written to offspring.txt.chr11.81792950.PDF
NOTICE: Processing sample offspring.txt CNV chr20:10511631-10583260 with copy number of 1 ... written to offspring.txt.chr20.10511631.PDF
NOTICE: Processing sample offspring.txt CNV chr3:3957986-4054960 with copy number of 1 ... written to offspring.txt.chr3.3957986.PDF

I wonder, what does this mean Use of uninitialized value in numeric gt (>) at C:\Users\andsav\Desktop\PennCNV-1.0.5\PennCNV-1.0.5\visualize_cnv.pl line 204. and how does it affect me?

Then, when I want to look at the generated plots, I was under the impresion that they will exist in jpg format in the folder. instead I have this

If I open one of them using Rstudio, it gives me the followin error
Error in file(file, "rt") : cannot open the connection
In addition: Warning messages:
1: file ‘.RData’ has magic number 'RDX3'
Use of save versions prior to 2 is deprecated
2: In file(file, "rt") :
cannot open file 'offspring.txt.chr11.81792950.signal': No such file or directory

Any ideas on what could be wrong and what I need to do to fix this?

System INFO
I use windows 10 x64, installed ActivePerl 5.8 x32 and have R 3.6.0

[nitzzzzzzz]

Hi andrisvAria,
Facing same issue. have you fixed it? if yes, how did you fix it? my system info is same as of you.
thanks

[andrisvAria]

Hey @nitzzzzzzz . Unfortunately I can't find the exact solution since it was such a long time ago. But, I do remember it was an issue with this library
[https://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html].

[nitzzzzzzz]

I just used jpeg r function [https://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html] instead of bitmap in cnv_visualize.pl like jpeg(filename=""Rplot%03d.jpeg"",width=3,height=3,units="in",res=300,pointsize=6) and the issue is resolved. Thank you andrisvAria for help *----------------------------------------* *----------------------------------------* *With Regards* *NITESH KUMAR SHARMA* *PhD Research Scholar (Bioinformatics)* *Centre For Agricultural Bioinformatics* *ICAR-Indian Agricultural Statistics Research Institute * *Library Avenue, Pusa, New Delhi, 110012* *Ph- (+91) 8506891991*

…

On Wed, Jan 12, 2022 at 4:12 PM andrisvAria ***@***.***> wrote: Hey @nitzzzzzzz <https://github.com/nitzzzzzzz> . Unfortunately I can't find the exact solution since it was such a long time ago. But, I do remember it was an issue with this library [https://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html]. — Reply to this email directly, view it on GitHub <#44 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AXHNQFSXP34LJ6DZSMHHSSLUVVLJPANCNFSM4HZRW7GQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[kaichop]

Thank you for the help addressing the issue. I am not very familiar with R, so I cannot really tell why sometimes PDF is not generated; it is good to know that PNG/JPG can work instead.