Cannot visualize in Scaffold Analysis on Panorama

[HoxB8]

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

[dmathew79]

Is there a resolution to the top question as I have experienced a similar issue?

[sreenathrajagopal]

Is there a resolution to the top question as I have experienced a similar issue?

Try Using the older version of the vite package for generating scaffold mapsvite-0.4.4.tar.gz

It worked for me to visualise the scaffold analysis on Panorama

[jessica4698]

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

Hello,
I also met the same problem that I couldn't visualize scaffold map on panorama::panorama(). Did you find any solution to visualize scaffold map successfully? I also tried to use older version of the vite package (0.4.4) for generating scaffold maps, but I still failed on panorama. I hope is there anyone who has solutionn for this problem? Thank you so much for your help.

[zming716]

It seems like that the names of landmarker nodes are setting wrong. You can open .graphml file manually and search for "v_name" and you will find that the string like "0" occurs more than once. Change these numbers following by "v_name" to make them unique. Hope this helps.