Comments (7)
mikejiang
commented on July 29, 2024
As long as fcs file generated conforms to the standard, cytolib should have no problem to parser it. Feel free to report it when it does
from cytoml.
malcook
commented on July 29, 2024
Apologies, my question was only poorly stated. I am really most interested in applying a gating strategy developed in FCSExpress under control of R, something akin to what flowWorkspace enables for flowjo workspaces. So far, I am successful in importing into an environment the .gatingML files (which recent versions of FCSExpress can export). I can identify the imported filters and apply them individually to a flowFrame or flowSet.
I am now building a GatingSet and using gs_pop_add to add to it each imported filter. In appreciation of your TIP that the standard gatingML mainly focuses on the definition of individual gates in a flat structure, which is really not suitable for representing the gating hierarchy from GatingSet, I am employing a naming convention for the gates to encode the hierarchy (or simple order) of gating (e.g. liveCells.1.0, singleCells.2.1, giving each named gate an index and the index of its parent) and thus how to structure the various calls to gs_pop_add .
Having done this, when I then recompute the GatingSet I (appropriately) get an error
Error in cpp_gating(x@pointer, y, alwaysLoadData, verbose, leaf.bool) :
colname not found: TransformsingleSS02-W.fcs.SS02-W
which makes sense because I have not (yet) learned how to add the transforms present in the gatingML to the GatingSet.
I am having trouble figuring out what my next steps should be. Perhaps examining the source for how the flowJo workspace import will give me the secret sauce I need at this point. But I would be grateful for any worked examples.
I am attaching an example .gatingML (which does not yet adhere to my proposed gate naming convention) and an .fcs file file if it helps you to help me.
21cy147.zip
Thanks
from cytoml.
altrabio
commented on July 29, 2024
Hi Malcolm,
I am wondering if you finally succeeded in importing an FCSExpress gating in R? If so, would you be able to share your code, it would so much helpful!
Thanks
from cytoml.
malcook
commented on July 29, 2024
Alas I stopped pursuing this line of approach but would be interested in learning of your or anyone else’s successes in such endeavors, or if perhaps the CytoML framework has improved support or documentation for such capabilities.
~ ***@***.***
From: altrabio ***@***.***>
Sent: Thursday, December 21, 2023 10:02 AM
To: RGLab/CytoML ***@***.***>
Cc: Cook, Malcolm ***@***.***>; Author ***@***.***>
Subject: Re: [RGLab/CytoML] FCS Express compatibility (Issue #139)
Hi Malcolm,I am wondering if you finally succeeded in importing an FCSExpress gating in R? If so, would you be able to share your code, it would so much helpful!Thanks—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authore
<https://us.report.cybergraph.mimecast.com/alert-details/?dep=d0SV6MS1TtzbJXHDX%2F8MIg%3D%3D1lZdlmIqjAvEpR9ZrigdDa08Y1lb6miQ5HUEg9j22I48No%2FBvWsWmHzUcmFpM%2BYOf7nejRmbrmrWOW4nzIEgymFkrT4iHHREsTcmLGSR9jHvt7qGl4WeKYUqWr4Ukun96USAlnaGm%2BEGx7EpFIacUKeErvl9%2BDLeG61tOV6toYtUcccTQIo0fKAbt7dIp4bwi6gxU9ai58FvNclhVwTTpTONJLhudRcjVsRxA1o%2B5fQVNZpk2NBJmS%2BbrGZYbH4KJ3KaXi45TQkOj3nsLYRHiuC8mG3TGxbFhk2NDJxKja4D58LrYaS2ybNwEnSADKjIGIVd%2FeUos6hu6i6I%2F5bSrKLCpXe2XCpQJw4vBy%2BGmW3okbocmLX3iGzXGDOk3GLqYp%2B4n5%2FCSZPAfjXAGroX3kzvQWYRh4molagMzBfhkNjotjYxr8H%2BtekhPCZoc2w15bfMekkHZkw7NBCrtGcrp4Yjl7GUSQpoH5T4BYsyj9w0UaSsAuZEo7S4VbA4CXFm4pEZQnVfMetgrNsGS1fQAg9W43Cmcq9FWOxmOgBkIGBjAQlWeKgW4TVPvptgJm25aUG%2B04ntMIAq6d%2Fh%2BuFPf86HTA83TP9tpA4RvsqhtGFPioRkEq2h6eXrJGptmYCjbyR7FEIdbugeuTKVpd74Lqf30xHuCyr%2Fw6V2ZFmlAR5uCSdWbfOX%2BqXeYpy1gzdaqg7YtG8SYCzqC7Oyjd%2BZvLl3I0zBHn78ew4Ckhd5HFMW%2B%2FwmGEehfGOrkNkxzzrEWXYybWMaVzjSIsoDW9uEiO3a66eCpxsgNzC4v0riKgAsleonJV87etmwl0Tj52JYUJ0WZr51889GoTq6bWTGjYGKKgWuSljXz6XqwBUPTQDx54WGtNTzjZCbqg%2BwAtxlM4Hf4Uj5FdYtEpkpmrrgfQ%3D%3D>
Hi Malcolm,
I am wondering if you finally succeeded in importing an FCSExpress gating in R? If so, would you be able to share your code, it would so much helpful!
Thanks
—
Reply to this email directly, view it on GitHub<#139 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AADWHOXMEQ2R4XUE75UQYTDYKRMQZAVCNFSM5G3NIYNKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBWGY2TMMRXGIYQ>.
You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>
from cytoml.
Related Issues (20)
- gs-to-flowjo parse error HOT 3
- gs_cyto_data and gatingset_to_flowjo, or how to update FCS files for flowjo export HOT 1
- try(eval(substitute(subset)), silent = TRUE) in flowjo_to_gatingset causes error when the subset argument is passed by lapply HOT 1
- CytoML Xml File Parsing Issues HOT 8
- Issue Parsing FlowJo (v10.7.2) XML File HOT 3
- Get indices of gated events from a FJ workspace / alternative to flowjo_to_gatingset HOT 5
- gs-to-flowjo Singularity issue HOT 2
- Ellipses coordinates are not correct in Gating Set after flowJo workspace parsing - v2.9.0 HOT 4
- R Session Aborts when calling flowjo_to_gatingset() more than once HOT 3
- gatingset_to_flowjo() fails with unsupported transformation: LIN
- Using FlowJo gating on pre-compensated, pre-transformed FCS files HOT 5
- flowjo_to_gatingset troubleshoot: "unknown tranformation type!transforms:linear" HOT 3
- flowjo_to_gatingset(), colname not found: error HOT 2
- Export populations as dataframe from a FlowJo workspace HOT 2
- extract inverse transform
- flowjo_to_gatingset does not accept data.frame as path HOT 5
- flowCore::read.FCS works but CytoML::flowjo_to_gatingset fails; no valid FCS file HOT 11
- boolean gate error
- Incompatible with Apple Silicon Mac HOT 7
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from cytoml.