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interactivereport / cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
https://cellxgenevip-ms.bxgenomics.com
MIT License
129 stars 44 forks source link

ggrastr & viridis R Packages Not Found #69

Closed trentleslie closed 2 years ago

trentleslie commented 2 years ago

Hi,

We are running a cellxgeneVIP instance on AWS, and I am having a couple issues when trying to generate volcano plots in VIP DEG and trying to generate density scatter plots in VIP Density Scatter.

In DEG, the error returned:

ERROR @server: Traceback (most recent call last):
  File "/home/*****/anaconda3/envs/VIP/lib/python3.8/site-packages/server/app/VIPInterface.py", line 57, in route
    taskRes = distributeTask(data["method"])(data)
  File "/home/*****/anaconda3/envs/VIP/lib/python3.8/site-packages/server/app/VIPInterface.py", line 731, in DEG
    raise SyntaxError("in volcano.R: "+res.stderr.decode('utf-8'))
  File "<string>", line None
SyntaxError: in volcano.R: Error in library(ggrastr) : there is no package called ‘ggrastr’
Execution halted

In Density Scatter, the error returned:

ERROR @server: Traceback (most recent call last):
  File "/home/*****/anaconda3/envs/VIP/lib/python3.8/site-packages/server/app/VIPInterface.py", line 57, in route
    taskRes = distributeTask(data["method"])(data)
  File "/home/*****/anaconda3/envs/VIP/lib/python3.8/site-packages/server/app/VIPInterface.py", line 1193, in DENS2D
    raise SyntaxError("in R: "+res.stderr.decode('utf-8'))
  File "<string>", line None
SyntaxError: in R: Error in loadNamespace(x) : there is no package called ‘viridis’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted

And a screenshot of the DEG issue:

image

It looks like a similar issue mentioned here, but there's no information about a solution there. Any suggestions on how to install/identify the packages needed? Thanks for any help!

Cheers, Trent

baohongz commented 2 years ago

Please follow this,

https://github.com/interactivereport/cellxgene_VIP#4-install-r-packages

If you don't have admin right, please use VIP_conda_R.yml at step 2.

trentleslie commented 2 years ago

Got it, I was using someone else's existing VIP install but didn't realize I needed to configure my own R environment on my end. Packages were installed using Step 4 and all is good, thank you for the quick response!