Open GKok opened 2 years ago
Hmmm... I think it is your selection criteria, can you include the printout of cyto_deatils(gs)
?
They're included in my opening post:
> head(cyto_details(gs))
name varX varY date varZ donor gene
A1 A1.fcs 100 100 05-04-2022 K0 xxx none
A2 A2.fcs 0 100 05-04-2022 K0 xxx none
A3 A3.fcs 100 1 05-04-2022 K0 xxx none
A4 A4.fcs 0 1 05-04-2022 K0 xxx none
A5 A5.fcs 100 1000 05-04-2022 K0 xxx none
A6 A6.fcs 0 1000 05-04-2022 K0 xxx none
Can you try setting select = 1
instead?
Same error.
> cyto_gate_draw(gs,
+ #select=list(name="A1.fcs"),
+ select=1,
+ parent = "root",
+ alias = "Cells",
+ channels = c("FSC-A","SSC-A"),
+ type = "polygon",
+ xlim = c(0,6000000),
+ ylim = c(0,8000000),
+ gatingTemplate = "gates.csv")
Error: Subset out of bounds
And if you remove select completely does it run?
No, still throws the same error.
Yeah OK it looks like the cyto_names()
may be out of sync with the rownames of cyto_details()
. I have already fixed this in the new version (coming soon), I can take a look tomorrow to see if I can patch it in the meantime.
Thank you, I really appreciate it.
@GKok I don't want to waste time fixing this for the current version. Perhaps in the meantime you could try running the following before gating:
cyto_details(gs)$name <- rownames(cyto_details(gs))
This should get everything back in sync and the gating should proceed.
Hi Dillon,
I've started using your package(s) again to analyse new data. I'm re-using a script from last year, which worked well, but with updated versions of all packages.
When drawing gates, I'm running into an unspecified problem. I can't find a solution online or here, on Github. Would you know what's going wrong?
My code:
The error:
Not sure if it helps, but the first lines of cyto_details:
Thank you,
Gautam