Dear Clustvis developer,

while I like the Web-version of Clustvis a lot, I often encounter problems with the server crashing or being unresponsive.
Trying to use the Docker Version does not work for me either. I am using Windows10.
Now, I have installed the R version, which works with the example provided. However, I could not find any documentation describing how to pass all the different parameters to the pipeline to customize the heatmaps.

Help would be appreciated.

Thanks
Matthias

Hi, firstly just want to say thanks for creating and maintaining an excellent tool.

I was hoping you could help me run your great app locally (the website can be a bit slow if I'm trying many variations).

I am new to Docker, but understand it to be a way of running controlled environments and fixed software versions. I haven't used it before. Unfortunately, I haven't quite got it running but hope that I'm close.

My process for installing

Running a Windows 10 machine, I downloaded docker for windows. From CMD prompt I downloaded the docker image using "docker pull taunometsalu/clustvis."

From within Docker, I installed ClustVis with the commands (entered verbatim in to CLI):

sudo docker pull taunometsalu/clustvis
mkdir ~/customClustvis/
cd ~/customClustvis/
wget https://github.com/taunometsalu/ClustVis/archive/master.zip
unzip master.zip
chmod -R go+rx ~/customClustvis/
sudo docker run -d
--name customClustvis
-p :3838
-v ~/customClustvis/ClustVis-master/:/srv/shiny-server/:ro
taunometsalu/clustvis

Now when I run from within docker, it says:

[2022-04-01 00:20:33.349] [INFO] shiny-server - Shiny Server v1.5.5.872 (Node.js v6.10.3)

[2022-04-01 00:20:33.351] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf"

[2022-04-01 00:20:33.374] [WARN] shiny-server - Running as root unnecessarily is a security risk! You could be running more securely as non-root.

[2022-04-01 00:20:33.376] [INFO] shiny-server - Starting listener on 0.0.0.0:3838

Unfortunately, that's as far as I got. I tried entering http:/0.0.0.0.3838 in to chrome and IE web browser (from my windows 10, not any linux version within CMD), but don't see any shiny app. I'm not sure how my Windows 10 interacts with the docker image. Do I need to install or run something else? Is it a mistake that the IP is showing as 0.0.0.0?

Thank you again.

Kind regards,
Richard

In using ClustVis for PCA within R, could you please tell me the command for exporting the variances each PC is responsible for? Thanks!

Hi,

I have run ClustVis container on windows successfully before. I recently updated docker and then removed the container and rerun it with the exact same command.
docker run -d --name customClustvisColor -p 7777:3838 -v C:\Users\baolongsu\Documents\customClustvis\ClustVis-master\:\srv\shiny-server\:ro taunometsalu/clustvis
But this time it's not working. When I go to the address, it opens a sample shiny welcome page. Can you help me with it?

Many thanks!

Dear Taunometsalu,

I am relatively new to R and try to get Clustvis to run. In principle it works. However, when I try to run the following:
proc = processData(imp, transformation = NA, annoColKeep = NULL,

•                annoColMethodAgg = "median", maxNaRows = 0.9999, maxNaCols = 0.9999,
  

•                remConstCols = FALSE, rowCentering = TRUE, rowScaling = "vector",
  

•                pcaMethod = "svdImpute", maxComponents = 100)
  

this error message appears:
Fehler in apply(anno, 1, function(x) paste0(x, collapse = ", ")) :
dim(X) must have a positive length

using annoColMethodAgg = NA, does not produce any problems.

???
Help would be appreciated.
Thanks
Matthias

ClustVis is curently not usable since several annotation files seem to be missing, such as clustvisInput_20150416_spec_hsapiens.RData and the related gprofOntos_* files. Kindly provide these files in the repository.

Hi, thanks for ClustVis as a means for getting a PCA analysis of data. The web-interface for the heatmap, however, hangs too often when changing parameters to adapt clustering method, figure and label sizes. Could you maybe provide examples in the Vignette how to set/change these values in an R-script/command so that someone can produce/alter figures independent of server- or web capacity straight from the R command line?

would it be possible to add a horizontal/vertical line at a specific position in the heatmap to separate groups? something similar to rowsep or colsep in heatmap.2

Thank you in advance for your help!

Hi,

I repeatedly get this error, too many open devices.

Please advise.

Thanks!

Hi there,

first of all thanks for sharing this platform and your knowlegde of course!
Either I use the normal or large editon tool, I keep getting disconnected after uploading my csv or tab files. I also tried to copy-paste it without success. I look Forward to your advice!
Thanks,
Dejan

Hi Tauno:
Thank you for the ClustVis package which is very helpful for my project!
I wish CustVis had another function (as pull-down menu) to subtract a list of genes of my interest. For example, at differential expression analysis there will be gene list for significantly expressed. If there is option that gene list could be pasted (or loaded from file which contains the gene list) and their expression level would be displayed in the main panel. This is quite similar to database query, but it seems do-able with a simpler way in ClustVis.
I failed to add this function to it as your ClustVis seems quite complicated project beyond my coding capability at this moment.

Hi, I am trying to access clustvis tool (http://biit.cs.ut.ee/clustvis/) but its not working. It opens the web page but no further process happening.

I used it many times earlier and its a very useful for my study, but now its not working.

Do there is any maintenance issue?

Please help me, I need it urgently.

Best regards

Great project! Is there any chance you'd be willing to add gene-based annotations, like for instance in the heatplus R package (PDF, page 13)? These annotation data could be added the same way in the input matrix as for the sample-based annotations, and also visualized identically (but on the Y axis). That would be of great value to highlight custom functional (e.g., pathway) groupings of genes, and see if they cluster well together.

Hi, I cannot access the ClustVis website and was wondering if it is down for maintenance? In this case, wuld it be possible to get an estimate when the site is up again? All best wishes, Jannto

, Zaragoza, Spain

Hello! I am using the Clust-vis web interface (Issues trying to use in R due to R package being newer) and every time I upload or paste data, I get a dark screen with the error message that I have been disconnected from the server, with a link to reload, with the same thing happening in the clust-vis large data version. It was working fine yesterday morning for the same data set, then for the last 24 hours about I have been consistently having the same issue.
Thank you so much!

Hello and THANK YOU for gluing these tools together!

I was wondering whether there exists a way to automate the tool? I know that I can put my own pipeline together that use these tools, but that would be kind of a waste seeing as that is basically what you have here. I was just wondering if one could or has implemented a way besides filling in a web form every time to configure and submit files to clustvis. I hope that I haven't just missed this in your documentation.

Thanks again!

Hi,
Trying to run the docker, I got this error:
The application failed to start.

The application exited during initialization.

-su: line 0: cd: /srv/shiny-server: Permission denied.

Any suggestions to solve the issue?

Thanks