Can't get Cerebro to Work with Shiny

[aelyaderani]

Wanted to try everything before I posted on here again haha 😅
Any help would be appreciated, Also talked to my colleague and once we have the data up and running I can share it with you so you can try our 300k cell 10x sample haha

So i followed all your steps from here https://romanhaa.github.io/cerebroApp/articles/host_cerebro_on_shinyapps.html

I've ran into some issues and can't get it to work. I attached some screen shots and a tree of my ~/test_cerebro_shinyapps

this is where i ran:
setRepositories(addURLs = c(BioC = "https://bioconductor.org/packages/3.11/bioc"))
rsconnect::deployApp('~/test_cerebro_shinyapps/', appName = 'Cerebro')

this is my app.R

this is my R Shiny web page and the error i get.

aelyaderani@pbc-cerebro:~/test_cerebro_shinyapps$ tree
.
├── app.R
├── extdata
│   ├── example_gene_set.gmt
│   ├── genes_mt_hg_ensembl.tsv.gz
│   ├── genes_mt_hg_gencode_v27.tsv.gz
│   ├── genes_mt_hg_name.tsv.gz
│   ├── genes_mt_mm_ensembl.tsv.gz
│   ├── genes_mt_mm_gencode_vM16.tsv.gz
│   ├── genes_mt_mm_name.tsv.gz
│   ├── genes_ribo_hg_ensembl.tsv.gz
│   ├── genes_ribo_hg_gencode_v27.tsv.gz
│   ├── genes_ribo_hg_name.tsv.gz
│   ├── genes_ribo_mm_ensembl.tsv.gz
│   ├── genes_ribo_mm_gencode_vM16.tsv.gz
│   ├── genes_ribo_mm_name.tsv.gz
│   ├── hg38_gene_ID_name.tsv.gz
│   ├── logo_Cerebro.png
│   ├── mm10_gene_ID_name.tsv.gz
│   └── v1.3
│   ├── example.crb
│   ├── pbmc_SCE.rds
│   └── pbmc_seurat.rds
├── rsconnect
│   └── shinyapps.io
│   └── klsnrna
│   └── Cerebro.dcf
└── shiny
└── v1.3
├── about
│   ├── UI.R
│   └── server.R
├── analysis_info
│   ├── UI.R
│   └── server.R
├── color_management
│   ├── UI.R
│   └── server.R
├── color_setup.R
├── enriched_pathways
│   ├── UI.R
│   ├── select_content.R
│   ├── server.R
│   └── table.R
├── extra_material
│   ├── UI.R
│   ├── content.R
│   ├── select_content.R
│   └── server.R
├── gene_expression
│   ├── UI.R
│   ├── expression_by_gene.R
│   ├── expression_by_group.R
│   ├── expression_by_pseudotime.R
│   ├── expression_in_selected_cells.R
│   ├── projection.R
│   ├── server.R
│   └── table_of_selected_cells.R
├── gene_id_conversion
│   ├── UI.R
│   └── server.R
├── groups
│   ├── UI.R
│   ├── cell_cycle.R
│   ├── composition.R
│   ├── expression_metrics.R
│   ├── select_group.R
│   ├── server.R
│   └── tree.R
├── load_data
│   ├── UI.R
│   ├── sample_info.R
│   ├── select_file.R
│   └── server.R
├── marker_genes
│   ├── UI.R
│   ├── select_content.R
│   ├── server.R
│   └── table.R
├── most_expressed_genes
│   ├── UI.R
│   ├── select_group.R
│   ├── server.R
│   └── table.R
├── overview
│   ├── UI.R
│   ├── projection.R
│   ├── selected_cells_plot.R
│   ├── selected_cells_table.R
│   └── server.R
├── plotting_functions.R
├── shiny_UI.R
├── shiny_server.R
├── trajectory
│   ├── UI.R
│   ├── distribution_along_pseudotime.R
│   ├── expression_metrics.R
│   ├── number_of_expressed_genes_by_state.R
│   ├── number_of_transcripts_by_state.R
│   ├── projection.R
│   ├── select_method_and_name.R
│   ├── selected_cells_table.R
│   ├── server.R
│   └── states_by_group.R
└── utility_functions.R

20 directories, 84 files

[romanhaa]

Hi @aelyaderani! I think I remember having had that same problem before. I'll have a look at it later today and let you know.

[aelyaderani]

thanks @romanhaa 😊 I'll take whatever help I can. I really want TGen (https://www.tgen.org/) to use cerebro as its primary data sharing with out collaborators... let me know if you are able to find the problem. thanks! :)

[romanhaa]

I was able to re-produce and fix it. It's actually quite simple, you only need to replace

Cerebro.options <- list(

with

Cerebro.options <<- list(

in the app.R file. This means the Cerebro.options variable will be assigned to the global environment. Let me know how if that solves it also for you.

EDIT: I updated the vignette accordingly.

[aelyaderani]

thanks! @romanhaa it worked perfect :)

[aelyaderani]

hi @romanhaa i was wandering if changing the Maximum upload size is different for the shiny host? i changed 800 to 2000. Is that correct? if so, i'm not sure why i'm getting that Message because the test .crb file i'm using is only 500MB :(

[romanhaa]

Hmm, that's strange. I'm wondering if shinyapps.io has any limits for file uploads. The alternative is that the options are not set correctly but I can't see any mistake.

Is the app hosted on port 1337? You should be able to see that from the log messages.

Can you try to set the max size for file uploads through options(shiny.maxRequestSize=2000*1024^2)? You can just add that line above or below the definition of shiny_options. It shouldn't make any difference but it might be worth a try.