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Question: Error in pcaplot3d from pcaExplorer, when running Deseq2 since update of packages
0
gravatar for reubenmcgregor88
3 months ago by
reubenmcgregor880 wrote:

Hi, 

I was plotting 3D PCA's from Desq2 output using simple:

> pcaplot3d(ddsMF, intgroup = "donor")

I then updated some packages:

> install.packages(c("httr", "Matrix", "plotrix", "shape", "shiny", "threejs", "tidyr"))

And now the pcaplot3D function returns this error:

Error in scatterplot3js(d[, 1:3], color = cols, renderer = "canvas", size = 1.3,  : 
  (list) object cannot be coerced to type 'double'

I have then run the same code on the same data on my computer at home, without updating packages, and it works well again.

Stupidly I then updated the packages and the same error popped up.

Any advice?

Thanks,

Reuben

platform       x86_64-apple-darwin15.6.0   
arch           x86_64                      
os             darwin15.6.0                
system         x86_64, darwin15.6.0        
status                                     
major          3                           
minor          4.1                         
year           2017                        
month          06                          
day            30                          
svn rev        72865                       
language       R                           
version.string R version 3.4.1 (2017-06-30)
nickname       Single Candle  

ADD COMMENTlink modified 3 months ago • written 3 months ago by reubenmcgregor880
1
gravatar for reubenmcgregor88
3 months ago by
reubenmcgregor880 wrote:

UPDATE:

For anyone having the same issue, it was the "threejs" package update that was messing with the output!

I installed the older version:

> require(devtools)

> install_version("threejs", version = "0.2.2", repos = "http://cran.us.r-project.org")

And then plot3dpca runs fine again,

I will try and report this but to threejs, but my experience getting through on here has not been great.

Thanks,

ADD COMMENTlink written 3 months ago by reubenmcgregor880

As a long term solution, I updated the code to the call for pcaplot3d which was using threejs.

The issue was related to some new major changes in rthreejs. It should be fixed now, as in https://github.com/federicomarini/pcaExplorer/commit/95422a244a183329bbd183785e3fef4be5d1ebe4. The changes would ideally propagate soon to both devel and release.

Federico

ADD REPLYlink written 12 weeks ago by Federico Marini90
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