xlim error when selecting " Toggle gff annotations"

[devonorourke]

Hi again folks,

Problem 1

I noticed a minor tweak needed to load the example data in the shinyGraphing directory in the server.R script on line 36:

thetas <- fread(input = path, sep = " ", header = TRUE)

While this command will work for outputs labelled graph.me, this fails to load the example provided in the tutorial package (BKN_Diversity.thetas.gz.pestPG ), nor will it work for any angsd-wrapper {out}.pest.PG output from ones own data. However, a short fix by substituting the delimiter to tab-separated will do the trick:

thetas <- fread(input = path, sep = "\t", header = TRUE)

...

Problem 2

Once the files were able to be uploaded, I could use all the various interactive features, clicking on different tests without issue, and zooming in on certain regions without any problem (what a cool tool!). While I can also upload a .gff file without registering an error, the second I click the box "Toggle GFF annotations" I get an error message as follows:

Warning: Error in plot.window: invalid 'xlim' value Stack trace (innermost first): 106: plot.window 105: localWindow 104: plot.default 103: plot 102: plot 101: renderPlot [/Users/devonorourke/Documents/Lab.Foster/bat_genomics/angsd_analyses/my_app/server.R#250] 91: <reactive:plotObj> 80: plotObj 79: origRenderFunc 78: output$thetaPlot2 1: runApp

Once the gff file is read, I can see the interval lines appear in the top panel of the interactive screen (blue hash marks along the x-axis), however the second panel which would normally generate the zoomed regions is no longer displayed. A message on the webpage displays "Error: invalid 'xlim' value".

I receive this error using the provided example Zea_mays.AGPv3.23.chromosome.10.gff3.gz file, and the same error when I select my own GFF file.

Thanks for any advice you can offer,

Cheers

[ChaochihL]

@devonorourke Thank you for providing feedback on our software!

Regarding Problem 1, the BKN_Diversity.thetas.gz.pestPG file in the shinyGraphing directory is used as the splash screen and was not meant to be uploaded again. For output files from the tutorial and running angsd-wrapper, the *.pestPG file and *.graph.me file are formatted slightly differently, so the *.pestPG file will not work if you upload it (unless you make changes to the code of course). Our intention was for users to upload the *.graph.me file since the software spits out multiple file extensions that could get confusing. I apologize for the confusion with file extension naming schemes. I will change the splash screen BKN_Diversity.thetas.gz.pestPG file extension name and edit the code appropriately to clarify that.

I am still working on Problem 2 and will get back to you once I have a fix.

[devonorourke]

Hi Chaochih, Any chance Problem 2 was resolved yet from this post? Thanks very much!