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kimpenn / PIVOT

Platform for Interactive analysis and Visualization Of Transcriptomics data
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error #17

Closed amitpande74 closed 4 years ago

amitpande74 commented 4 years ago

Hi, I pulled PIVOT from Docker. When I upload my gene count table it does not accept it and issues a warning: Warning: The 'plotly_relayout' event tied a source ID of 'range_filter_plotly' is not registered. In order to obtain this event data, please add event_register(p, 'plotly_relayout') to the plot (p) that you wish to obtain event data from. What is the wrong step I am doing here. Kindly inform. regards.

qinzhu commented 4 years ago

Can you double check if your gene count table is same format as the example table (https://rawgit.com/qinzhu/PIVOT/master/inst/app/www/manual_file.html#46_load_example_dataset), and contains no NA values? You can ignore the plotly warning.

amitpande74 commented 4 years ago

Hi @qinzhu , It is not very clear from the screenshot that you have provided in the link . A normal count matrix has gene names as rows and the columns have sample values. Can you kindly have a look at the file I have and whether this is correct as a input file or should it be wrangled further. regards.

example

qinzhu commented 4 years ago

The file looks correct. It looks like the data is already normalized so please make sure the Normalization method is selected as "none". Also please check if any of the entries contain no value. I also attached an example file here so you can compare.

Counts (normalized).csv.zip

amitpande74 commented 4 years ago

Same error. I tried uploading your file as well. Please specify input file and it stops.

qinzhu commented 4 years ago

There's something wrong with the latest shiny. I'm still investigating but I found the temporary solution is once you launch PIVOT, refresh the page, then load data. Sorry for the inconvenience.

eturkes commented 4 years ago

Hi @qinzhu I see you've been making commits to try to fix the issue. Please let me know when you're all done and I'll update the Docker image!

qinzhu commented 4 years ago

The bug can be fixed via installing previous version of shiny: devtools::install_version("shiny", version = "1.3.0", repos = "http://cran.us.r-project.org") # Latest shiny 1.4.0 has bug in module reactivity I've updated the install instruction. @eturkes Appreciate it! I think only the shiny version needs to be fixed.

eturkes commented 4 years ago

@qinzhu , great, an updated Docker image is now available with the previous version of shiny. Will be automatically pulled when using the command in the README.

amitpande74 commented 4 years ago

@eturkes @qinzhu Thanks a lot for looking into the problem. @qinzhu there are still errors while I got while running the data: Warning: Error in : 'plotQC' is not an exported object from 'namespace:scater' 172: stop 171: getExportedValue 170: :: 169: renderPlot 167: func 127: drawPlot 113: 97: drawReactive 84: origRenderFunc 83: output$scater_feature_plot 3: shiny::runApp 2: pivot_main 1: pivot Warning: Error in biomaRt::getBM: Invalid attribute(s): entrezgene Please use the function 'listAttributes' to get valid attribute names 79: stop 78: biomaRt::getBM 74: observeEventHandler 3: shiny::runApp 2: pivot_main 1: pivot Kindly help.

eturkes commented 4 years ago

Docker image has been updated with the entrezgene fix.