mageck test failed at creating a complete pdf file in a paired design

[BingbingYuan]

Thanks for creating this wonderful package. It worked great for me before. I have a project with a paired design recently. When I when ran mageck test with --paired --pdf, I got the following error messages: $ mageck test -k data.txt -t treat_1,treat_2 -c control_1,control_2 --paired --pdf -n treat_vs_control

Error in axis(1, at = 1:length(vali), labels = (collabel), las = 2) : 'at' and 'labels' lengths differ, 2 != 4 Execution halted

The same command worked fine without --pdf. The error message occurred during the plotting in the R script. Thanks,

[davidliwei]

Hi Bingbing, can you use the RMD file to generate a html file instead? We ran into a lot of problems on the --pdf option and this function is going to retire in future versions. Thank you!

[BingbingYuan]

Yes. I created a HTML file with my RMD file, and it looks really nice. I noticed that the output said top 5 genes, only the top 4 genes were displayed in the graph. It's related to "targetgenelist_neg=gstable[gstable[,6]<5,1]", should be <=5 instead. I can change the number of genes myself within the script. I just thought that you might like to know. Thanks a lot for your quick response! It's quite helpful!

On Thu, Nov 19, 2020 at 2:04 PM Wei Li notifications@github.com wrote:

Hi Bingbing, can you use the RMD file to generate a html file instead? We ran into a lot of problems on the --pdf option and this function is going to retire in future versions. Thank you!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/davidliwei/mageck/issues/2#issuecomment-730575393, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACI44XWQTIYBP7R2WQA5VFTSQVT2HANCNFSM4T3X4JDA .

-- Bingbing

[davidliwei]

Great, thanks! Will fix it soon.