can only visualize the "Test page"

[dalloliogm]

Hello,
I've followed the instructions in the tutorial. However, when I open the server page, I can only see a "Test page" message.

What am I doing wrong?

episerver = createServer(
  #port=as.numeric(Sys.getenv("CDSW_PUBLIC_PORT")), 
  verbose=T,
  try_ports=T,
  daemonized=T)
# start the server
episerver$start_server()
episerver

### Start the epivizr app
#
# The epivizr app should connect to the episerver.
#
# You can specify the Epiviz server using the episerver variable defined above, or manually specify host and http_port
#
# For a full tutorial on epivizr, see http://bioconductor.org/packages/release/bioc/vignettes/epivizr/inst/doc/IntroToEpivizr.html 
epi = startEpiviz(
            #host=Sys.getenv("CDSW_IP_ADDRESS"),
   #         host=Sys.getenv("CDSW_IP_ADDRESS"),
            open_browser=F,
          server = episerver)
epi

Moreover, when I print the episerver or epiclient variables, I get a "not connected" message:

> episerver
<EpivizServer> port: 8080, not connected 

[jkanche]

Hello @dalloliogm, are you using this with the epivizr package ?

[dalloliogm]

Hi,
yes, I am. In the example above, I am loading epivizr and epivizrServer. Thanks for the answer.

[jkanche]

if you use the epivizr package, you do not need to explicitly create the server. Once you start an epivizr session, it automatically creates an instance of the epivizrServer.

library(epivizr)
library(antiProfilesData)
library(SummarizedExperiment)
app <- startEpiviz(workspace="qyOTB6vVnff", gists="2caf8e891201130c7daa")
blocks_chart <- app$plot(tcga_colon_blocks, datasource_name="450k colon_blocks")
app$stop_app()

for more examples, please see the vignettes from the epivizr package. Let me know if you still have issues.

[dalloliogm]

Thanks... unfortunately I still get the "Not Connected" error, when copying&pasting the code from your post:

Epiviz App connection:
Server: <EpivizServer> port: 7123, not connected 

Measurements:
                   id              name length connected columns
1 450k colon_blocks_1 450k colon_blocks    129

[jkanche]

We've seen this happen with a few users before where they use enterprise laptops and the user has limited access to opening ports. Another way to test this might be to see if you can run a shiny app locally ? Also after running the startEpiviz function, does the app open the browser ? Opening the browser is necessary to establish the initial connection between the browser and the R-session.

[harrica]

I am working with gio on trying to get this working on our system. When I execute the example a browser window opens but at the following location
http://epiviz.cbcb.umd.edu/4/index.php?websocket-host[]=ws://localhost:7123&debug=false&ws=qyOTB6vVnff&gist[]=2caf8e891201130c7daa&useCookie=true&settings=default&

is that the correct behaviour?

[jkanche]

yes, opening the browser connects it with the R-session. Now you can visualize datasets from the R-session with the browser. If you would like to run everything locally, we have another package called epivizrStandalone. The API is very similar to epivizr but everything is run locally instead of our hosted web browser.

[harrica]

Excellent I'll give that a try this afternoon. thank you very much

[dalloliogm]

Thank you,
I've tried epivizrStandAlone and I was able to visualize something. It opened a browser on the local machine, which I can access from other machines.

library(epivizrStandalone)
library(Homo.sapiens)
app <- startStandalone(Homo.sapiens, 
                       keep_seqlevels=paste0("chr",c(1:22,"X","Y")), 
                       verbose=TRUE, 
                       use_viewer_option = TRUE,
                       non_interactive=F, host="10.137.232.212", try_ports=T)

However the browser is empty.. no genes and no chromosomes. Is that normal? Is there a guide to describe how to add them?
Moreover, the browser dies after a while, with the message:

Error in .wait_until_connected(app$server) : 
  [epivizrStandalone] Error starting app. UI unable to connect to websocket server.

I saw that there is also an epiviz project, with an application that runs via docker. I can start that without many issues, however I can't send data to it from R.

Apologies if this is already documented, I am a bit lost among the epiviz packages :-). Thanks for the great work, anyway.

[jkanche]

Hello, We modularized our packages so that it is easier to use them across different projects. The packages that the end user would use would be either epivizr or epivizrStandalone. both these packages use the R-session to act as a backend webserver responding to requests from the UI and serve data loaded into the R-session. the packages differ where the UI is run from - epivizr package uses the UI hosted here at UMD (http://epiviz.cbcb.umd.edu) whereas the epivizrStandalone package downloads the UI locally from Github and serves the application.

I made a short screencast of the epivizrStandalone running inside Rstudio's viewer using some example datasets (I use chr11 because the sample datasets only contain data in this region).
https://www.loom.com/share/00aca7b2bc3a41278b0b2af74bed85dd

the code from the screencast

library(epivizrStandalone)
library(Homo.sapiens)

app <- startStandalone(Homo.sapiens, 
                       keep_seqlevels=paste0("chr",c(1:19,"X","Y")), 
                       chr="chr11",
                       start=110081455,
                       end=135006517,
                       verbose=TRUE, 
                       use_viewer_option = TRUE)

## load sample datasets
data("tcga_colon_blocks")
data("tcga_colon_curves")
data("tcga_colon_expression")

app$plot(tcga_colon_blocks, datasource_name = "tcga 450K blocks")
app$plot(tcga_colon_curves, datasource_name = "tcga 450K methylation", type="bp", 
         columns=c("cancerMean", "normalMean"))
## stops the app and removes the datasets from the UI
app$stop_app()

looking at your code, I think using the host= "10.137.232.212" might be causing the issue. Can you try this without this parameter ? Sorry for the confusion on the packages and This helps us get better at documenting. Let me know if you continue to have issues.

[harrica]

I've run the above and it opens a blank EpiViz4 page and I get the following errors

app <- startStandalone(Homo.sapiens,

•                    keep_seqlevels = paste0("chr",c(1:19,"X","Y")),
  

•                    chr="chr11",
  

•                    start=110081455,
  

•                    end=135006517,
  

•                    verbose=TRUE)
  

checking for updates to epiviz app...
Starting Epivizr!
Initializing session manager...
Opening connections...
Done starting Epivizr!
Starting epiviz websocket connection
Opening browser
Using url http://127.0.0.1:7123/epivizr-standalone.html?websocket-host[]=ws://127.0.0.1:7123&debug=false&useCookie=false&
Error in .wait_until_connected(app$server) :
[epivizrStandalone] Error starting app. UI unable to connect to websocket server.

data("tcga_colon_blocks")
data("tcga_colon_curves")
data("tcga_colon_expression")
app$plot(tcga_colon_blocks,datasource_name = "tcga 450K blocks")
Error in app$plot(tcga_colon_blocks, datasource_name = "tcga 450K blocks") :
Error adding measurements for data object
app$plot(tcga_colon_curves,datasource_name = "tcga 450K methylation",type="bp",

•      columns=c("cancerMean","normalMean"))
  

Error in app$plot(tcga_colon_curves, datasource_name = "tcga 450K methylation", :
Error adding measurements for data object

Any ideas?

[jkanche]

hello @harrica, can you run

setStandalone() before you execute the code snippet from the previous post ? Can you post the error if you see one ? Also can you post the sessionInfo() of the machine you are running this on ?

[harrica]

here it is

setStandalone()
cloning epiviz from git...
cloning into '/home/rh682900/R/x86_64-redhat-linux-gnu-library/3.3/epivizrStandalone/www'...
Receiving objects: 1% (126/12514), 60 kb
Receiving objects: 11% (1377/12514), 742 kb
Receiving objects: 21% (2628/12514), 3253 kb
Receiving objects: 31% (3880/12514), 16227 kb
Receiving objects: 41% (5131/12514), 21858 kb
Receiving objects: 51% (6383/12514), 29217 kb
Receiving objects: 61% (7634/12514), 30513 kb
Receiving objects: 71% (8885/12514), 44527 kb
Receiving objects: 81% (10137/12514), 44879 kb
Receiving objects: 91% (11388/12514), 45295 kb
Receiving objects: 100% (12514/12514), 46099 kb, done.
[1] "/home/rh682900/R/x86_64-redhat-linux-gnu-library/3.3/epivizrStandalone/www"

sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods
[9] base

other attached packages:
[1] antiProfilesData_1.10.0 Homo.sapiens_1.3.1
[3] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 org.Hs.eg.db_3.4.0
[5] GO.db_3.4.0 OrganismDbi_1.16.0
[7] GenomicFeatures_1.26.4 GenomicRanges_1.26.4
[9] GenomeInfoDb_1.10.3 AnnotationDbi_1.36.2
[11] IRanges_2.8.2 S4Vectors_0.12.2
[13] epivizrData_1.2.0 Biobase_2.34.0
[15] BiocGenerics_0.20.0 epivizrServer_1.2.0
[17] epivizrStandalone_1.2.0 epivizr_2.4.1

loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 git2r_0.25.2 BiocInstaller_1.24.0
[4] pillar_1.3.1 XVector_0.14.1 bitops_1.0-6
[7] tools_3.3.3 zlibbioc_1.20.0 biomaRt_2.30.0
[10] digest_0.6.12 bit_1.1-12 lattice_0.20-35
[13] RSQLite_2.0 memoise_1.1.0 tibble_2.1.1
[16] pkgconfig_2.0.2 rlang_0.3.4 graph_1.52.0
[19] Matrix_1.2-10 DBI_0.7 rstudioapi_0.6
[22] yaml_2.1.14 rtracklayer_1.34.2 Biostrings_2.42.1
[25] grid_3.3.3 bit64_0.9-7 R6_2.2.2
[28] RBGL_1.50.0 XML_3.98-1.9 BiocParallel_1.8.2
[31] blob_1.1.0 Rsamtools_1.26.2 GenomicAlignments_1.10.1
[34] SummarizedExperiment_1.4.0 mime_0.5 httpuv_1.3.3
[37] RCurl_1.95-4.8 crayon_1.3.4 rjson_0.2.20

[jkanche]

does running the script after setStandalone() work now ? If not are you running this on rstudio locally or on a remote machine ?

[harrica]

I get the same error, its running on a remote rstudio. I will attempt it locally on my Mac tomorrow