Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

flowjo_to_gatingset(), colname not found: error #148

Open
KammannT opened this issue Oct 21, 2022 · 2 comments
Open

flowjo_to_gatingset(), colname not found: error #148

KammannT opened this issue Oct 21, 2022 · 2 comments

Comments

@KammannT
Copy link

Hi,
I am struggling to parse a flowjo.wsp file containing all the compensation and gating for my fcs files.

library(CytoML)
fcs_dir <- 'PathtoFolderoffcsfiles'
wsp_file <- 'PathtoFlowjowspfile'
flow <- CytoML::open_flowjo_xml(wsp_file)

The workspace can be loaded and indicates number of samples, groups, keywords, etc.

test <-CytoML::flow_to_gatingset(flow, path=fcs_dir, name=1)

line above gives the error:
"Error in (function (ws, group_id, subset, execute, path, cytoset, backend_dir, :
colname not found: Comp-BV605-CD161"

Loading a .xml file of the same Flowjo workspace (instead of .wsp) gives a different error but can however save the file:

xml_file <- 'PathtoFlowjoxmlfile'
flow2 <- CytoML::open_flowjo_xml(xml_file)

Error message:
^namespace error: Namespace prefix data-type on fas-dimension is not defined
<data-type:fcs-dimension data-type:name="Comp-BUV737-CD69"^

test2 <-CytoML::flow_to_gatingset(flow2, path=fcs_dir, name=1)

line above gives the error:
Error in (function (ws, group_id, subset, execute, path, cytoset, backend_dir, :
*: unknown tranformation type!transforms:linear

Support is very much appreciated! Thanks

@mikejiang
Copy link
Member

What if you choose second group?i.e. name=2

@KammannT
Copy link
Author

What if you choose second group?i.e. name=2

Gives exactly the same error:
"Error in (function (ws, group_id, subset, execute, path, cytoset, backend_dir, :
colname not found: Comp-BV605-CD161"

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants