Open upatel2 opened 2 years ago
diva_to_gatingset
function has an argument worksheet
, can be set to either "normal" or "global". The latter use the global worksheet as the template, thus doesn't require fcs info.
@mikejiang Thank you for clarifying that. I was actually also encountering another issue. I am not sure whether this is due to my XML file or whether it is about errors in my code.
library(flowWorkspace) library(flowWorkspaceData) library(CytoML) workspace <- ('C:/Users/utsav/Documents/Patient4Template.xml') qw <- open_diva_xml(workspace) qw Diva Workspace Version Version 8.0.1 File location: C:/Users/utsav/Documents File name: Patient4Template.xml Workspace is open.
Groups in Workspace Error in names(x) <- value : 'names' attribute [2] must be the same length as the vector [1]
Are you able to please help me find a way through this?
Thank You!
Please provide a reproducible example for me to troubleshoot
@mikejiang Hi Mike,
As the file I am working with is for research, I have asked my supervisors if I can send this to you. Should they respond yes, I can email it to you.
Can you please share your email until I wait for their response?
Thank You!
mike@ozette.ai
sorry it took a while for me to get back to you. Looks like the current diva parser does require the normal worksheet that is associated with some fcs file to be present in order to proceed the global template worksheet parsing.
i.e. it expects something like
and yours seem to be the pure template that doesn't have
data_filename
field.
I am not sure if we have the bandwidth or resource to add this support. The workaround for you is to create some dummy normal worksheet to associate with one fcs in diva software and then re-export the xml so that diva parser will not error out.
No. You don't want to manually edit this XML. This file is supposed to be generated and exported from diva software. What you need to do is to use diva software to recreate the analysis by adding both global and normal worksheet the normal worksheet should be associated with a particular fcs file.So that this will get our diva parser working properly. But real gates can be still stored in global worksheet as a template
Hi,
I am working closely with .xml and .fcs files for research regarding extracting gates from a particular XML file.
I have followed your tutorial on GitHub regarding parsing a DIVA workspace file (i.e., extdata/diva/PE_2.xml) and it seems to work fine for me. However, when I try to parse a local XML file that I have on my local drive, I get this error:
Diva Workspace Version Version 8.0.1 File location: . File name: Patient4Template.xml Workspace is open.
Groups in Workspace Error in names(x) <- value : 'names' attribute [2] must be the same length as the vector [1]
I am not sure why I am getting this error and I can't seem to solve this particular issue.
Also, I wanted to ask another question regarding how your XML file has the correlated FCS file details. The XML file I have does not contain any fcs file detail, so is it still possible to extract gates from it? Or is that not possible?
It would be great if you can help me with understanding the issue I am having.
Thank You very much, Utsav