parkerici / panorama Goto Github PK

Hello,

I have samples from four organs (bone marrow, spleen, blood, and liver) and would like to generate Scaffold maps of the 4 organs on one reference map. I pooled and clustered the data using the cluster_fcs_files_groups. I then used Vite to load landmarks and generated a Scaffold Result folder of .graphml files. I open the Panorama GUI and set the folder to where the .graphml files are located. When I try to choose one of the .graphml files, I encounter the following error. I appreciate any insights on how to troubleshoot this.

R version 4.1.1

Warning: non-unique value when setting 'row.names': ‘0’
No traceback available
Warning: Error in .rowNamesDF<-: duplicate 'row.names' are not allowed
53: stop
52: .rowNamesDF<-
51: row.names<-.data.frame
49: rownames<-
48: igraph::get.data.frame
47: panorama:::get_vertex_attributes
46: [C:/Users/liusuy/Dropbox/My PC (PATH-577183-DT)/Documents/R/win-library/4.1/panorama/shinyGUI/server/tab_graph.R#191]
3:
1: panorama::panorama
Warning: non-unique value when setting 'row.names': ‘0’
No traceback available
Warning: Error in .rowNamesDF<-: duplicate 'row.names' are not allowed
105: stop
104: .rowNamesDF<-
103: row.names<-.data.frame
101: rownames<-
100: igraph::get.data.frame
99: panorama:::graph_to_json
98: reactive:output$graphui_mainnet [C:/Users/liusuy/Dropbox/My PC (PATH-577183-DT)/Documents/R/win-library/4.1/panorama/shinyGUI/server/tab_graph.R#218]
82: output$graphui_mainnet
3:
1: panorama::panoram

Hi,

I have been trying to make scatter/boxplots in panorama, and i cant make it work. I feel i have tried any conceivable combination of things ticked or markers chosen. I want to look at a functional marker p38 in my three groups: baseline/4h/24h. i have these three samples from 6 patients, a total of 18 files. What am i doing wrong? And how do i get the heatmap?

HI Federico, I was using panorama and got this error.

Warning: Error in panorama:::plot_clusters: clusters_data directory is missing, data cannot be plotted

Where precisely does the clusters_data directory belong? in parallel with the clustered directory, or within it? Or somewhere else?
I was using the GUI for grappolo, vite, and panorama, in MacOS.

I'm unable to load the .graphml file output from Vite in Panorama. I get the above error (details below), and I have tinkered with my inputs in Premessa and Grappolo in a number of ways. I have also tried with and without metadata, as well as another set of FCS files to determine if a file is corrupt (neither seem to resolve the issue).

I've noticed that while Grappolo allows me to select parameters I want used to cluster, Vite does not allow me to select parameters for the analysis and runs only when no markers are selected.

Could this be a problem with the Vite package? I have existing .graphml files that can be visualized using Panorama so perhaps this is an issue with the Vite package.

Listening on http://127.0.0.1:8072
12: execCallbacks(timeoutSecs, all)
11: run_now(timeoutMs/1000, all = FALSE)
10: service(timeout)
9: serviceApp()
8: ..stacktracefloor..(serviceApp())
7: withCallingHandlers(expr, error = doCaptureStack)
6: globals$domain$wrapSync(expr)
5: promises::with_promise_domain(createStackTracePromiseDomain(),
expr)
4: captureStackTraces({
while (!.globals$stopped) {
..stacktracefloor..(serviceApp())
Sys.sleep(0.001)
}
})
3: ..stacktraceoff..(captureStackTraces({
while (!.globals$stopped) {
..stacktracefloor..(serviceApp())
Sys.sleep(0.001)
}
}))
2: shiny::runApp(appDir = file.path(system.file(package = "vite"),
"shinyGUI"), ...)
1: vite::vite_GUI()
Warning: Error in data.frame: arguments imply differing number of rows: 0, 2
103: stop
102: data.frame
101: cbind
100: cbind
99: panorama:::graph_to_json
98: reactive:output$graphui_mainnet [/Library/Frameworks/R.framework/Versions/3.5/Resources/library/panorama/shinyGUI/server/tab_graph.R#218]
82: output$graphui_mainnet
3:
1: panorama

last one, i promise...
when using Shift+click or Alt+click to select or deselect nodes in panorama, I have noticed that sometimes the node will refuse to be de-selected, and other times the program has developed a "memory", and will ignore my de-selection command when making heat maps or box plots. any ideas on how to fix? This is in a MacOS environment, High Sierra 10.13. I can post more details if necessary.

Hi,
when generating the heatmap of communities in the second window, in panorama, I noticed that the lower edge (where the marker names are written) gets cut off and one cannot scroll down any farther to see them. Is there a way to adjust this in the code? This might be another PC-> Mac complication.
Thanks!
Will post a photo of bug shortly...

Hi

I can't find where my mistake is. I have repeated every step of the flow-analysis-tutorial with no problem until I try to run panorama::panorama() on either my ubuntu terminal or RStudio.

In RStudio I get this message:

Warning: Error in [[: subscript out of bounds
48: getSliderType
47: updateSliderInput
46: [/home/juan/R/x86_64-pc-linux-gnu-library/3.4/panorama/shinyGUI/server/tab_graph.R#315]
3:
1: panorama::panorama

Any clue is much appreciate.

Cheers
Juan

Hi, I'm new to this package, and got it from one paper about brain cancer, using this package to visualize cytometry data. It's powerful and very useful for flow data analysis.

And my question is is it possible to analyze single cell RNA-seq data by this package?

Since data format, preprocessing pipeline could be some different between flow data and scRNAseq data, I wonder the accessibility to use it in scRNA-seq analysis.

Dear Pier,
I started to use Scaffold not long time ago. I have an issue to save/export created plot in package panorama(). Is it any smart way to do when I run analysis using GUI version? Or shall I run the script from R environment?
Thank you in advance for your reply!